Viral Load as Predictor of Crimean-Congo Hemorrhagic Fever Outcome

We used quantitative real-time reverse transcription–PCR to measure viral load in serum from 24 patients in Kosovo who had acute Crimean-Congo hemorrhagic fever. Viral load correlated with clinical disease and antibodies and could be used as a predictor of disease outcome

The complete genome sequence of a Crimean-Congo Hemorrhagic Fever virus isolated from an endemic region in Kosovo

The Balkan region and Kosovo in particular, is a well-known Crimean-Congo hemorrhagic fever (CCHF) endemic region, with frequent epidemic outbreaks and sporadic cases occurring with a hospitalized case fatality of approximately 30%. Recent analysis of complete genome sequences of diverse CCHF virus strains showed that the genome plasticity of the virus is surprisingly high for an arthropod-borne virus. High levels of nucleotide and amino acid differences, frequent RNA segment reassortment and even RNA recombination have been recently described. This diversity illustrates the need to determine the complete genome sequence of CCHF virus representatives of all geographically distinct endemic areas, particularly in light of the high pathogenicity of the virus and its listing as a potential bioterrorism threat. Here we describe the first complete CCHF virus genome sequence of a virus (strain Kosova Hoti) isolated from a hemorrhagic fever case in the Balkans. This virus strain was isolated from a fatal CCHF case, and passaged only twice on Vero E6 cells prior to sequence analysis. The virus total genome was found to be 19.2 kb in length, consisting of a 1672 nucleotide (nt) S segment, a 5364 nt M segment and a 12150 nt L segment. Phylogenetic analysis of CCHF virus complete genomes placed the Kosova Hoti strain in the Europe/Turkey group, with highest similarity seen with Russian isolates. The virus M segments are the most diverse with up to 31 and 27% differences seen at the nt and amino acid levels, and even 1.9% amino acid difference found between the Kosova Hoti and another strain from Kosovo (9553-01). This suggests that distinct virus strains can coexist in highly endemic areas

Functional shift with maintained regenerative potential following portal vein ligation

Selective portal vein ligation (PVL) allows the two-stage surgical resection of primarily unresectable liver tumours by generating the atrophy and hypertrophy of portally ligated (LL) and non-ligated lobes (NLL), respectively. To evaluate critically important underlying functional alterations, present study characterised in vitro and vivo liver function in male Wistar rats (n = 106; 210-250 g) before, and 24/48/72/168/336 h after PVL. Lobe weights and volumes by magnetic resonance imaging confirmed the atrophy-hypertrophy complex. Proper expression and localization of key liver transporters (Ntcp, Bsep) and tight junction protein ZO-1 in isolated hepatocytes demonstrated constantly present viable and well-polarised cells in both lobes. In vitro taurocholate and bilirubin transport, as well as in vivo immunohistochemical Ntcp and Mrp2 expressions were bilaterally temporarily diminished, whereas LL and NLL structural acinar changes were divergent. In vivo bile and bilirubin-glucuronide excretion mirrored macroscopic changes, whereas serum bilirubin levels remained unaffected. In vivo functional imaging (indocyanine-green clearance test; (99mTc)-mebrofenin hepatobiliary scintigraphy; confocal laser endomicroscopy) indicated transitionally reduced global liver uptake and -excretion. While LL functional involution was permanent, NLL uptake and excretory functions recovered excessively. Following PVL, functioning cells remain even in LL. Despite extensive bilateral morpho-functional changes, NLL functional increment restores temporary declined transport functions, emphasising liver functional assessment

Assessing the effects of Ang-(1-7) therapy following transient middle cerebral artery occlusion

The counter-regulatory axis, Angiotensin Converting Enzyme 2, Angiotensin-(1-7), Mas receptor (ACE2/Ang-1-7/MasR), of the renin angiotensin system (RAS) is a potential therapeutic target in stroke, with Ang-(1-7) reported to have neuroprotective effects in pre-clinical stroke models. Here, an extensive investigation of the functional and mechanistic effects of Ang-(1-7) was performed in a rodent model of stroke. Using longitudinal magnetic resonance imaging (MRI) it was observed that central administration of Ang-(1-7) following transient middle cerebral artery occlusion (MCAO) increased the amount of tissue salvage compared to reperfusion alone. This protective effect was not due to early changes in blood brain barrier (BBB) permeability, microglia activation or inflammatory gene expression. However, increases in NADPH oxidase 1 (Nox1) mRNA expression were observed in the treatment group compared to control. In order to determine whether Ang-(1-7) has direct cerebrovascular effects, laser speckle contrast imaging (LSCI) was performed to measure dynamic changes in cortical perfusion following reperfusion. Delivery of Ang-(1-7) did not have any effect on cortical perfusion following reperfusion however; it showed an indication to prevent the ‘steal phenomenon’ within the contralateral hemisphere. The comprehensive series of studies have demonstrated a moderate protective effect of Ang-(1-7) when given alongside reperfusion to increase tissue salvage

Drug trafficking in mice: In vivo functions of OATP uptake and ABC efflux transporters

In recent years, there has been increasing attention for drug uptake transporters of the Organic Anion-Transporting Polypeptide (human OATP, mouse Oatp, gene names SLCO, Slco) superfamily. Especially the OATP1A and OATP1B subfamilies turn out to have important physiological and pharmacological functions. Members of the OATP1A/1B subfamilies have received most interest because of their localization in tissues important for detoxification and pharmacokinetics (i.e. liver, small intestine and kidney) and their ability to mediate the cellular uptake of a wide variety of endogenous compounds but also many xenobiotics. OATP1A/1B transporters play important roles in the physiological detoxification by the liver of endogenous compounds, but also in determining tissue distribution, the rate and route of elimination, systemic exposure and oral bioavailability of drugs. In this thesis we studied OATP transporters in vivo using knockout mouse strains lacking all Oatp1a/1b transporters, and humanized transgenic mouse strains with liver-specific expression of human OATP1A2, OATP1B1 or OATP1B3. The concomitant use of these different mouse models is required because mouse and human OATP1A/1B proteins are not straightforward orthologues and their tissue localization and substrate specificity can differ substantially. Using these mice, we gained more insight into the physiological functions of OATP1A/1B, for instance the plasma clearance of unconjugated bilirubin and bile acids by facilitating their liver uptake. Further, we focussed on the pharmacological functions of these transporters in the plasma clearance (by efficient hepatic uptake) of statin drugs (pravastatin, rosuvastatin) and anticancer drugs (irinotecan/SN-38 and docetaxel). These findings have pharmacogenetic implications because there are several low-activity polymorphisms of OATP1A/1B transporters known. Also, complete deficiencies of either OATP1B1 or OATP1B3 transporters have been found in humans in addition to the Rotor syndrome patients, which completely lack both OATP1B1 and OATP1B3. All these individuals might be at risk of developing toxicities when treated with OATP1B substrates. Also co-administration of these drugs with OATP1A/1B inhibiting drugs might lead to clinically relevant drug-drug interactions. Human OATP1A/1B transporters are also expressed in several types of tumors and can thus confer sensitivity to anticancer drugs in cell lines overexpressing these transporters. Based on our findings that OATP1A/1B transporters transport several anticancer drugs in vivo we can speculate that they might mediate the tumor uptake of these anticancer drugs, and therefore modulate response to chemotherapy. We also studied the main ATP binding cassette (ABC) efflux transporters, ABCB1 (P-gp) and/or ABCG2 and their effect on the brain accumulation and oral bioavailability of tamoxifen and axitinib. We have found that endoxifen, a 100-fold more active metabolite of tamoxifen, is a P-gp substrate in vitro and in vivo. High expression of P-gp in breast tumors treated with tamoxifen might thus lead to insufficient intratumoral endoxifen concentrations and therefore insufficient therapeutic response. In the case of the tyrosine kinase inhibitor axitinib, we observed that Abcg2 has a role in limiting its bioavailability after oral administration, while at the blood-brain barrier, P-gp is the main determinant of axitinib brain penetration. These results might have clinical relevance for brain tumors positioned behind an intact and functional blood-brain barrier

Drug trafficking in mice: In vivo functions of OATP uptake and ABC efflux transporters

In recent years, there has been increasing attention for drug uptake transporters of the Organic Anion-Transporting Polypeptide (human OATP, mouse Oatp, gene names SLCO, Slco) superfamily. Especially the OATP1A and OATP1B subfamilies turn out to have important physiological and pharmacological functions. Members of the OATP1A/1B subfamilies have received most interest because of their localization in tissues important for detoxification and pharmacokinetics (i.e. liver, small intestine and kidney) and their ability to mediate the cellular uptake of a wide variety of endogenous compounds but also many xenobiotics. OATP1A/1B transporters play important roles in the physiological detoxification by the liver of endogenous compounds, but also in determining tissue distribution, the rate and route of elimination, systemic exposure and oral bioavailability of drugs. In this thesis we studied OATP transporters in vivo using knockout mouse strains lacking all Oatp1a/1b transporters, and humanized transgenic mouse strains with liver-specific expression of human OATP1A2, OATP1B1 or OATP1B3. The concomitant use of these different mouse models is required because mouse and human OATP1A/1B proteins are not straightforward orthologues and their tissue localization and substrate specificity can differ substantially. Using these mice, we gained more insight into the physiological functions of OATP1A/1B, for instance the plasma clearance of unconjugated bilirubin and bile acids by facilitating their liver uptake. Further, we focussed on the pharmacological functions of these transporters in the plasma clearance (by efficient hepatic uptake) of statin drugs (pravastatin, rosuvastatin) and anticancer drugs (irinotecan/SN-38 and docetaxel). These findings have pharmacogenetic implications because there are several low-activity polymorphisms of OATP1A/1B transporters known. Also, complete deficiencies of either OATP1B1 or OATP1B3 transporters have been found in humans in addition to the Rotor syndrome patients, which completely lack both OATP1B1 and OATP1B3. All these individuals might be at risk of developing toxicities when treated with OATP1B substrates. Also co-administration of these drugs with OATP1A/1B inhibiting drugs might lead to clinically relevant drug-drug interactions. Human OATP1A/1B transporters are also expressed in several types of tumors and can thus confer sensitivity to anticancer drugs in cell lines overexpressing these transporters. Based on our findings that OATP1A/1B transporters transport several anticancer drugs in vivo we can speculate that they might mediate the tumor uptake of these anticancer drugs, and therefore modulate response to chemotherapy. We also studied the main ATP binding cassette (ABC) efflux transporters, ABCB1 (P-gp) and/or ABCG2 and their effect on the brain accumulation and oral bioavailability of tamoxifen and axitinib. We have found that endoxifen, a 100-fold more active metabolite of tamoxifen, is a P-gp substrate in vitro and in vivo. High expression of P-gp in breast tumors treated with tamoxifen might thus lead to insufficient intratumoral endoxifen concentrations and therefore insufficient therapeutic response. In the case of the tyrosine kinase inhibitor axitinib, we observed that Abcg2 has a role in limiting its bioavailability after oral administration, while at the blood-brain barrier, P-gp is the main determinant of axitinib brain penetration. These results might have clinical relevance for brain tumors positioned behind an intact and functional blood-brain barrier

Prediktion av Behandlingsmisslyckande och Avhopp i en Online Intervention för Alkoholbrukssyndrom : Användning av Maskininlärning och Naturlig Språkbehandling för Prediktion av Behandlingsutfall

Alcohol Use Disorder (AUD), a clinical diagnosis defined in the DSM-5 by 11 criteria that span harmful use and dependence (see Section 2.1), is a global problem. In 2019 alone, alcohol consumption contributed to around 2.6 million deaths (4.7% of all deaths globally), and over 400 million people lived with alcohol use disorders. In the last 20 years, Internet-delivered Cognitive Behavioral Therapy (ICBT) has emerged as an effective treatment for AUD. However, the public health impact of ICBT is limited by high rates of non-response and dropout. A promising solution to this problem is the use of predictive models to identify patients at risk before treatment begins, enabling adaptive treatment strategies that can lead to improved treatment outcomes. Unfortunately, previous research in this field suggests that these models typically show moderate performance, with AUC scores in the 0.60-0.70 range. Prior research relies on structured data, such as severity ratings (e.g., the number of standard drinks). An advantage of ICBT is that unstructured text data is automatically collected, but there has not been much work on using unstructured text data for prediction purposes. This thesis investigated whether the use of text from motivational interviewing (MI), a novel data source in this context, could improve the prediction of non-response and dropout in an ICBT intervention for AUD. The data used in this study comes from a randomized controlled trial of ICBT for AUD. We compared the effects of various feature sets on performance using nested cross-validation and took steps to prevent data leakage. Logistic Regression (LR) and XGBoost models were trained on baseline characteristics (e.g., questionnaire data and demographics), text-derived features from topic modeling, and a combination of both. Additionally, a cutting-edge approach based on few-shot fine-tuning of Sentence Transformers (SetFit) for text classification was used to predict treatment outcomes using the raw text data from MI. Lastly, we trained LR and XGBoost on a combination of baseline characteristics and UMAP-reduced SetFit embeddings. The results show that the MI text, whether we trained models on text-derived features or used the SetFit framework, exhibited no predictive power, with performance metrics hovering around the chance level. Instead, baseline characteristics were the most predictive of treatment outcomes. The simpler LR model consistently outperformed the more complex XGBoost model, achieving an AUC of 0.705 for non-response and 0.648 for dropout using baseline data. Combining baseline data with text-derived features led to marginal and inconsistent improvements. Consistent with previous research, the findings suggest that current measurement practices in clinical psychology and psychiatry, which focus on collecting baseline characteristics, yield moderate performance (AUC 0.60-0.70) when treatment outcomes are 12 weeks away. The findings also show that the text from MI used in this study does not contain enough predictive information to improve upon this, regardless of model complexity. The primary conclusion of this study is that the key to improving the performance of predictive models in clinical psychology and psychiatry lies in collecting and training models on data with greater predictive power rather than relying solely on baseline characteristics or developing more sophisticated machine learning models. Future research could investigate how dynamic in-treatment data, which captures patients’ behaviors and experiences in real time, impacts performance.Alkoholbrukssyndrom, en DSM-5-diagnos som omfattar både riskbruk, skadligt bruk och beroende (se Avsnitt 2.1), är ett globalt problem. Enbart under 2019 bidrog alkoholkonsumtion till cirka 2,6 miljoner dödsfall (4,7% av alla dödsfall globalt), och över 400 miljoner människor levde med alkoholbrukssyndrom. Under de senaste 20 åren har internetlevererad kognitiv beteendeterapi (IKBT) etablerats som en effektiv behandling för alkoholbrukssyndrom. IKBT:s inverkan på folkhälsan begränsas dock av höga nivåer av behandlingsmisslyckande och avhopp. En lovande lösning på detta problem är användningen av prediktiva modeller för att identifiera patienter som riskerar att inte bli bättre eller hoppa av innan behandlingen påbörjas, vilket möjliggör anpassningsbara behandlingsstrategier som kan leda till förbättrade behandlingsutfall. Tyvärr visar tidigare forskning inom området att sådana modeller vanligtvis uppnår en måttlig prestationsnivå, med AUC-värden i intervallet 0,60-0,70. Tidigare studier har främst förlitat sig på strukturerad data, såsom skattningar av problemens svårighetsgrad (t.ex. antal standardglas). En fördel med IKBT är att ostrukturerad textdata samlas in automatiskt, men det finns begränsat med forskning kring hur denna typ av data kan användas för prediktiva syften. Denna avhandling undersökte huruvida text från motiverande samtal (MS), en ny datakälla i detta sammanhang, kan förbättra förutsägelser av behandlingsmisslyckande och avhopp i en IKBT-intervention för alkoholbrukssyndrom. Studien baserades på data från en randomiserad kontrollerad studie av IKBT för alkoholbrukssyndrom. Vi jämförde effekterna av olika typer av data på modellprestation med hjälp av nested cross-validation och vidtog åtgärder för att förhindra dataläckage. Logistisk Regression (LR) och XGBoost-modeller tränades på baslinjedata (t.ex. frågeformulär och demografi), textbaserade variabler samt en kombination av båda. Därtill användes en modern metod baserad på few-shot fine-tuning av Sentence Transformers (SetFit) för textklassificering, i syfte att förutsäga behandlingsutfall med hjälp av råtext från MS. Slutligen tränades LR och XGBoost på en kombination av baslinjedata och UMAP-reducerade SetFit-inbäddningar. Resultaten visar att MS-texten, oavsett om modellerna tränades på textbaserade variabler eller med SetFit-ramverket, inte uppvisade någon prediktiv kraft, med prestationsmått nära chansnivå. I stället visade sig baslinjedata vara mest prediktiva för behandlingsutfall. Den enklare LR-modellen presterade bättre än den mer komplexa XGBoost-modellen och uppnådde en AUC på 0,705 för behandlingsmisslyckande och 0,648 för avhopp, baserat på baslinjedata. Kombinationen av baslinjedata och textbaserad information ledde till marginella och inkonsekventa förbättringar. I linje med tidigare forskning antyder resultaten att nuvarande mätpraxis inom klinisk psykologi och psykiatri – med fokus på insamling av baslinjedata – leder till måttlig förmåga att förutsäga behandlingsutfall 12 veckor framåt i tiden. Resultaten visar också att texten från MS i denna studie inte innehåller tillräcklig prediktiv information för att förbättra denna förmåga, oavsett modellens komplexitet. Studiens huvudsakliga slutsats är att nyckeln till att förbättra prediktiva modellers prestation inom klinisk psykologi och psykiatri ligger i att samla in och träna modeller på data med högre prediktivt värde, snarare än att enbart förlita sig på traditionsenlig baslinjedata eller utveckla mer sofistikerade maskininlärningsmodeller. Framtida forskning skulle kunna undersöka hur dynamisk data insamlad under behandling – som fångar patienters beteenden och upplevelser i realtid – påverkar modellernas prestation

Att underlätta övergången från blockbaserad programmering inom utbildning

Many learners find the transition from block-based programming to text-based programming difficult. Consequently, research has investigated how block-based languages support learners when making the transition to text-based programming. It categorized the way in which block-based languages support the transition into one-way transition, dual-modality and hybrid environments. This research investigates how one-way transition environments compare to dual-modality environments with regards to learning a text-based language, and how the two modalities differ with regards to the motivational factors satisfaction, enjoyment and easiness. The results show that dual-modality environments could be a better alternative than one-way transition environment when learners make the transition from block-based to text-based programming. The results also show that solving a problem in dual-modality environments could be easier than solving them in one-way transition environments, which could potentially mean that learners experience more motivation when making the transition in a dual-modality environment. This study also investigated if there is an alternative to one-way transition, dual-modality and hybrid environments when helping learners transition from block-based to text-based programming, and what a learning activity in this alternative solution could look like. It found that Blockly Games is an alternative, and describes a learning activity built in Blockly Games. Future research should aim at gaining a deeper understanding of the differences between one-way transition, dual-modality and hybrid environments, and investigate if the approach taken by Blockly Games is a better alternative.Många elever tycker att övergången från blockbaserad programmering till textbaserad programmering är svår. Följaktligen har forskning undersökt hur blockbaserade språk stödjer elever när de gör övergången till textbaserad programmering. En studie fann att blockbaserade språk stöder denna övergång med hjälp av one-way transition miljöer, dual-modality miljöer och hybrid miljöer. Denna forskning undersöker hur one-way transition miljöer jämför sig med dual-modality miljöer när det kommer till att lära sig ett textbaserat språk, och hur de två modaliteterna skiljer sig åt med avseende på motivationsfaktorerna tillfredsställelse, njutning och lätthet. Resultaten visar att dual-modality miljöer kan vara ett bättre alternativ än one-way transition miljöer när eleverna gör övergången från blockbaserad till textbaserad programmering. Resultaten visar också att det kan vara lättare att lösa ett problem i dual-modality miljöer än att lösa dem i one-way transition miljöer, vilket potentiellt kan innebära att eleverna upplever mer motivation när de gör övergången i en dual-modality miljö. Denna studie undersökte också om det finns ett alternativ till one-way transition miljöer, dual-modality miljöer och hybrid miljöer när elever ska övergå från blockbaserad till textbaserad programmering, och hur en inlärningsaktivitet i denna alternativa lösning skulle kunna se ut. Den fann att Blockly Games är ett alternativ och beskriver en inlärningsaktivitet byggd i Blockly Games. Framtida forskning borde försöka få en djupare förståelse för skillnaderna mellan one-way transition miljöer, dual-modality miljöer och hybrid miljöer, och undersöka om det tillvägagångssätt som Blockly Games använder är ett bättre alternativ

Att underlätta övergången från blockbaserad programmering inom utbildning

Many learners find the transition from block-based programming to text-based programming difficult. Consequently, research has investigated how block-based languages support learners when making the transition to text-based programming. It categorized the way in which block-based languages support the transition into one-way transition, dual-modality and hybrid environments. This research investigates how one-way transition environments compare to dual-modality environments with regards to learning a text-based language, and how the two modalities differ with regards to the motivational factors satisfaction, enjoyment and easiness. The results show that dual-modality environments could be a better alternative than one-way transition environment when learners make the transition from block-based to text-based programming. The results also show that solving a problem in dual-modality environments could be easier than solving them in one-way transition environments, which could potentially mean that learners experience more motivation when making the transition in a dual-modality environment. This study also investigated if there is an alternative to one-way transition, dual-modality and hybrid environments when helping learners transition from block-based to text-based programming, and what a learning activity in this alternative solution could look like. It found that Blockly Games is an alternative, and describes a learning activity built in Blockly Games. Future research should aim at gaining a deeper understanding of the differences between one-way transition, dual-modality and hybrid environments, and investigate if the approach taken by Blockly Games is a better alternative.Många elever tycker att övergången från blockbaserad programmering till textbaserad programmering är svår. Följaktligen har forskning undersökt hur blockbaserade språk stödjer elever när de gör övergången till textbaserad programmering. En studie fann att blockbaserade språk stöder denna övergång med hjälp av one-way transition miljöer, dual-modality miljöer och hybrid miljöer. Denna forskning undersöker hur one-way transition miljöer jämför sig med dual-modality miljöer när det kommer till att lära sig ett textbaserat språk, och hur de två modaliteterna skiljer sig åt med avseende på motivationsfaktorerna tillfredsställelse, njutning och lätthet. Resultaten visar att dual-modality miljöer kan vara ett bättre alternativ än one-way transition miljöer när eleverna gör övergången från blockbaserad till textbaserad programmering. Resultaten visar också att det kan vara lättare att lösa ett problem i dual-modality miljöer än att lösa dem i one-way transition miljöer, vilket potentiellt kan innebära att eleverna upplever mer motivation när de gör övergången i en dual-modality miljö. Denna studie undersökte också om det finns ett alternativ till one-way transition miljöer, dual-modality miljöer och hybrid miljöer när elever ska övergå från blockbaserad till textbaserad programmering, och hur en inlärningsaktivitet i denna alternativa lösning skulle kunna se ut. Den fann att Blockly Games är ett alternativ och beskriver en inlärningsaktivitet byggd i Blockly Games. Framtida forskning borde försöka få en djupare förståelse för skillnaderna mellan one-way transition miljöer, dual-modality miljöer och hybrid miljöer, och undersöka om det tillvägagångssätt som Blockly Games använder är ett bättre alternativ