HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.

To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the 'Phylogenetics and Networks for Generalised HIV Epidemics in Africa' consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai Community Cohort Study, n=2,833; MRC/UVRI Uganda, n=701; Mochudi Prevention Project, n=359; Africa Health Research Institute Resistance Cohort, n=92). Next-generation sequencing success rates varied: more than 80% of the viral genome from the gag to the nef genes could be determined for all sequences from South Africa, 75% of sequences from Mochudi, 60% of sequences from MRC/UVRI Uganda, and 22% of sequences from Rakai. Partial sequencing failure was primarily associated with low viral load, increased for amplicons closer to the 3' end of the genome, was not associated with subtype diversity except HIV-1 subtype D, and remained significantly associated with sampling location after controlling for other factors. We assessed the impact of the missing data patterns in PANGEA-HIV sequences on phylogeny reconstruction in simulations. We found a threshold in terms of taxon sampling below which the patchy distribution of missing characters in next-generation sequences has an excess negative impact on the accuracy of HIV-1 phylogeny reconstruction, which is attributable to tree reconstruction artifacts that accumulate when branches in viral trees are long. The large number of PANGEA-HIV sequences provides unprecedented opportunities for evaluating HIV-1 transmission dynamics across sub-Saharan Africa and identifying prevention opportunities. Molecular epidemiological analyses of these data must proceed cautiously because sequence sampling remains below the identified threshold and a considerable negative impact of missing characters on phylogeny reconstruction is expected

LHCb upgrade software and computing : technical design report

This document reports the Research and Development activities that are carried out in the software and computing domains in view of the upgrade of the LHCb experiment. The implementation of a full software trigger implies major changes in the core software framework, in the event data model, and in the reconstruction algorithms. The increase of the data volumes for both real and simulated datasets requires a corresponding scaling of the distributed computing infrastructure. An implementation plan in both domains is presented, together with a risk assessment analysis

Physics case for an LHCb Upgrade II - Opportunities in flavour physics, and beyond, in the HL-LHC era

The LHCb Upgrade II will fully exploit the flavour-physics opportunities of the HL-LHC, and study additional physics topics that take advantage of the forward acceptance of the LHCb spectrometer. The LHCb Upgrade I will begin operation in 2020. Consolidation will occur, and modest enhancements of the Upgrade I detector will be installed, in Long Shutdown 3 of the LHC (2025) and these are discussed here. The main Upgrade II detector will be installed in long shutdown 4 of the LHC (2030) and will build on the strengths of the current LHCb experiment and the Upgrade I. It will operate at a luminosity up to 2×1034 cm−2s−1, ten times that of the Upgrade I detector. New detector components will improve the intrinsic performance of the experiment in certain key areas. An Expression Of Interest proposing Upgrade II was submitted in February 2017. The physics case for the Upgrade II is presented here in more depth. CP-violating phases will be measured with precisions unattainable at any other envisaged facility. The experiment will probe b → sl+l−and b → dl+l− transitions in both muon and electron decays in modes not accessible at Upgrade I. Minimal flavour violation will be tested with a precision measurement of the ratio of B(B0 → μ+μ−)/B(Bs → μ+μ−). Probing charm CP violation at the 10−5 level may result in its long sought discovery. Major advances in hadron spectroscopy will be possible, which will be powerful probes of low energy QCD. Upgrade II potentially will have the highest sensitivity of all the LHC experiments on the Higgs to charm-quark couplings. Generically, the new physics mass scale probed, for fixed couplings, will almost double compared with the pre-HL-LHC era; this extended reach for flavour physics is similar to that which would be achieved by the HE-LHC proposal for the energy frontier

Measurement of branching fractions of charmless four-body Λ⁰_b and Ξ⁰_b decays

A search for charmless four-body decays of Λ b 0 and Ξ b 0 baryons with a proton and three charged mesons (either kaons or pions) in the final state is performed. The data sample used was recorded in 2011 and 2012 with the LHCb experiment and corresponds to an integrated luminosity of 3 fb−1. Six decay modes are observed, among which Λ b 0  → pK−π+π−, Λ b 0  → pK−K+K−, Ξ b 0  → pK−π+π− and Ξ b 0  → pK−π+K− are established for the first time. Their branching fractions (including the ratio of hadronisation fractions in the case of the Ξ b 0 baryon) are determined relative to the Λ b 0  → Λ c + π− decay

Study of the doubly charmed tetraquark T+cc

Quantum chromodynamics, the theory of the strong force, describes interactions of coloured quarks and gluons and the formation of hadronic matter. Conventional hadronic matter consists of baryons and mesons made of three quarks and quark-antiquark pairs, respectively. Particles with an alternative quark content are known as exotic states. Here a study is reported of an exotic narrow state in the D0D0π+ mass spectrum just below the D*+D0 mass threshold produced in proton-proton collisions collected with the LHCb detector at the Large Hadron Collider. The state is consistent with the ground isoscalar T+cc tetraquark with a quark content of ccu⎯⎯⎯d⎯⎯⎯ and spin-parity quantum numbers JP = 1+. Study of the DD mass spectra disfavours interpretation of the resonance as the isovector state. The decay structure via intermediate off-shell D*+ mesons is consistent with the observed D0π+ mass distribution. To analyse the mass of the resonance and its coupling to the D*D system, a dedicated model is developed under the assumption of an isoscalar axial-vector T+cc state decaying to the D*D channel. Using this model, resonance parameters including the pole position, scattering length, effective range and compositeness are determined to reveal important information about the nature of the T+cc state. In addition, an unexpected dependence of the production rate on track multiplicity is observed

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Chirurgisches Outcome und mikrobielle Besiedelung standardisierter Abstrichlokalisationen nach Pankreaskopfresektion (PPPD) bei chronischer Pankreatitis und Pankreaskopfkarzinom

Es wurde die These aufgestellt, dass Patienten mit Pankreaskopfkarzinom (CA) aufgrund der Schwere der Tumorerkrankung einen reduzierteren Allgemein- sowie Immunstatus als Patienten mit chronischer Pankreatitis (CP) aufweisen und sich dies im frühpostoperativen Outcome nach „Pylorus-erhaltender Pankreaskopfresektion nach Traverso-Longmire“ widerspiegelt, welcher Patienten beider Grunderkrankungen unterzogen wurden. Mit dem Ziel der Eruierung des Einflusses der unterschiedlichen Diagnosen wurde das postoperative Outcome aller konsekutiven Patienten, die der OP in einem definierten Untersuchungszeitraum an der Klinik für Allgemein-, Viszeral-, Gefäß- und Transplantationschirurgie des Universitätsklinikums Magdeburg A.ö.R. unterzogen worden waren, erfasst und gegenüberstellend ausgewertet. Das Outcome wurde durch die allgemeine und spezielle Komplikationsrate als Parameter der postoperativen Morbidität, die Letalität, „Surgical Site Infections“ (SSI) und die mikrobielle Besiedelungsrate mit -spektrum charakterisiert. Zwischen 2002-2015 wurden von 308 operierten Patienten n=282 Akten ausgewertet, davon 192 Fälle mit CA (68,1 %) und 90 Fälle mit CP (31,9 %). Die Grunderkrankung hatte mit Ausnahme von SSI, für die CA ein Risikofaktor war, keinen signifikanten Einfluss auf das frühpostoperative Outcome, Patienten mit CA hatten jedoch zusätzlich tendenziell höhere Besiedlungs- und allgemeine Komplikationsraten. Signifikante Risikofaktoren in der multivariaten Analyse waren außerdem das männliche Geschlecht für SSI und die mikrobielle Besiedelung sowie intraoperativ transfundierte Erythrozytenkonzentrate für die Letalität, die allgemeine und spezielle Komplikationsrate sowie operative Revisionen. Damit wurde ein teils signifikanter, teils tendenzieller nachteiliger Einfluss der Grunderkrankung CA gegenüber der CP auf das frühpostoperative Outcome aufgezeigt, insbesondere im Hinblick auf SSI nach PPPD. Dieser Einfluss wird durch die internationale Literatur bekräftigt

Stigma surrounding sexually transmitted Infections among medical students in Germany

Stigmatization by health care professionals leads to decreased help-seeking behaviors in those being stigmatized. Prejudicial attitudes are especially pronounced concerning sexually transmitted infections (STIs), which is crucial in light of rising prevalence rates of STIs in recent years. We aimed to examine stigmatization against patients with sexually versus non-sexually transmitted infections among medical students in Germany. We also assessed how a person’s sexual orientation or gender might contribute to stigma. Medical students (N = 332) read about a fictious patient with symptoms of pharyngitis after having had a casual sex encounter. Gender (female/male) and sexual orientation (hetero-/bi-/homosexual) of the patient as well as the pathogen causing the infection (gonococcus/H1N1-virus) were randomly varied. Afterwards, stigma against the patient was assessed. Patients with a gonococcal pharyngitis were perceived as more prone to engage in risky behavior, dumber, and less responsible than patients with a H1N1-virus pharyngitis. Bisexual patients were perceived as more prone to engage in risky behavior than hetero- and homosexual individuals. The predictability of the consequences of the patient’s actions was rated higher in bisexual patients. Stigmatizing attitudes toward patients with a STI were frequent, especially against bisexual patients. More education should be dedicated to sexual/LGB health during medical school to reduce existing stigma

IPA: Internet Personal Assistant

The Internet Personal Assistant (IPA) gives you the power to automatically act on data from the Internet. Create triggers to text you when it starts to snow in your zipcode or email your friend when their soccer team loses. Go even further by creating complex conditions and actions or even build you own data sources and actions to completely customize your triggers. URL website http://cs.carleton.edu/cs_comps/1112/news_agent/final_results/index.htm

Surgical Outcome and Microbial Colonization of Standardized Smear Locations after Pancreatic Head Resection (Pylorus-Preserving Pancreatoduodenectomy, PPPD) for Chronic Pancreatitis and Pancreatic Head Carcinoma

Introduction: Patients with chronic pancreatitis (CP) as well as with pancreatic head carcinoma (CA) undergo the surgical intervention named &ldquo;pylorus-preserving pancreatoduodenectomy according to Traverso&ndash;Longmire (PPPD)&rdquo;, which allowed a comparative analysis of the postoperative courses. The hypothesis was that patients with CA would have worse general as well as immune status than patients with CP due to the severity of the tumor disease and that this would be reflected in the more disadvantageous early postoperative outcome after PPPD. Methods: With the aim of eliciting the influence of the different diagnoses, the surgical outcome of all consecutive patients who underwent surgery at the Dept. of General, Abdominal, Vascular and Transplant Surgery at the University Hospital at Magdeburg between 2002 and 2015 (inclusion criterion) was recorded and comparatively evaluated. Early postoperative outcome was characterized by general and specific complication rate indicating morbidity, mortality, and microbial colonization rate, in particular surgical site infection (SSI, according to CDC criteria). In addition, microbiological findings of swabs and cultures from all compartments as well as preoperative and perioperative parameters from patient records were retrospectively documented and used for statistical comparison in this systematic retrospective unicenter observational study (design). Results: In total, 192 cases with CA (68.1%) and 90 cases with CP (31.9%) met the inclusion criteria of this study. Surprisingly, there were similar specific complication rates of 45.3% (CA) vs. 45.6% (CP; p = 0.97) and in-hospital mortality, which differed only slightly at 3.65% (CA) vs. 3.3% (CP; p = 0.591); the overall complication rate tended to be higher for CA at 23.4% vs. 14.4% (CP; p = 0.082). Overall, potentially pathogenic germs were detected in 28.9% of all patients in CP compared to 32.8% in CA (p = 0.509), and the rate of SSI was 29.7% (CA) and 24.4% (CP; p = 0.361). In multivariate analysis, CA was found to be a significant risk factor for the development of SSI (OR: 2.025; p = 0.048); the underlying disease had otherwise no significant effect on early postoperative outcome. Significant risk factors in the multivariate analysis were also male sex for SSI and microbial colonization, and intraoperatively transfused red cell packs for mortality, general and specific complications, and surgical revisions. Conclusions: Based on these results, a partly significant, partly trending negative influence of the underlying disease CA, compared to CP, on the early postoperative outcome was found, especially with regard to SSI after PPPD. This influence is corroborated by the international literature