Correlation Clustering with Low-Rank Matrices

Correlation clustering is a technique for aggregating data based on qualitative information about which pairs of objects are labeled 'similar' or 'dissimilar.' Because the optimization problem is NP-hard, much of the previous literature focuses on finding approximation algorithms. In this paper we explore how to solve the correlation clustering objective exactly when the data to be clustered can be represented by a low-rank matrix. We prove in particular that correlation clustering can be solved in polynomial time when the underlying matrix is positive semidefinite with small constant rank, but that the task remains NP-hard in the presence of even one negative eigenvalue. Based on our theoretical results, we develop an algorithm for efficiently "solving" low-rank positive semidefinite correlation clustering by employing a procedure for zonotope vertex enumeration. We demonstrate the effectiveness and speed of our algorithm by using it to solve several clustering problems on both synthetic and real-world data

A rapid quantitative colorimetric determination of blood acetone applied to the assessment of ketosis in fasted pregnant ewes

A simple, accurate, colorimetric method for determining blood acetone as an adjunct to the enzymic method of estimating the other ketones was developed and tested on a group of fasted pregnant ewes. Acetone reacted with 2-hydroxybenzaldehyde to form a stable coloured complex that followed Beer's Law up to an acetone concentration of at least 4 mg/ 100 ml of the test solution at 490 nm. While the optimum incubation time of the reaction mixture was found to be 3 h at 40 °C, it could also be left to incubate overnight at room temperature. When tested in a blood matrix, the method gave a mean within-batch coefficient of variation of 0,7%, and a day to day variation of 0, 3 – 1,2 %, while an overall recovery of 100,6 ± 1,4% was achieved over 5 concentration ranges (2,86 - 10,53 mg/100ml). The values obtained from this method corresponded closely to those from the diffusion technique previously employed and it considerably simplified the procedure. A direct linear relationship, y= 2,594x + 2,917 with a coefficient of determination r²= 0,958 for 49 pairs of data, was found between the acetone (= x mg/100 ml) and total ketone (= y mg/100 ml) concentrations in blood samples drawn from fasted pregnant sheep. This relationship can therefore be used to estimate accurately the degree of ketosis from the blood acetone concentration alone.The articles have been scanned in colour with a HP Scanjet 5590; 600dpi. Adobe Acrobat XI Pro was used to OCR the text and also for the merging and conversion to the final presentation PDF-format

Bacteremia During the First Year After Solid Organ Transplantation: An Epidemiological Update.

BACKGROUND There are limited contemporary data on the epidemiology and outcomes of bacteremia in solid organ transplant recipients (SOTr). METHODS Using the Swiss Transplant Cohort Study registry from 2008 to 2019, we performed a retrospective nested multicenter cohort study to describe the epidemiology of bacteremia in SOTr during the first year post-transplant. RESULTS Of 4383 patients, 415 (9.5%) with 557 cases of bacteremia due to 627 pathogens were identified. One-year incidence was 9.5%, 12.8%, 11.4%, 9.8%, 8.3%, and 5.9% for all, heart, liver, lung, kidney, and kidney-pancreas SOTr, respectively (P = .003). Incidence decreased during the study period (hazard ratio, 0.66; P < .001). One-year incidence due to gram-negative bacilli (GNB), gram-positive cocci (GPC), and gram-positive bacilli (GPB) was 5.62%, 2.81%, and 0.23%, respectively. Seven (of 28, 25%) Staphylococcus aureus isolates were methicillin-resistant, 2/67 (3%) enterococci were vancomycin-resistant, and 32/250 (12.8%) GNB produced extended-spectrum beta-lactamases. Risk factors for bacteremia within 1 year post-transplant included age, diabetes, cardiopulmonary diseases, surgical/medical post-transplant complications, rejection, and fungal infections. Predictors for bacteremia during the first 30 days post-transplant included surgical post-transplant complications, rejection, deceased donor, and liver and lung transplantation. Transplantation in 2014-2019, CMV donor-negative/recipient-negative serology, and cotrimoxazole Pneumocystis prophylaxis were protective against bacteremia. Thirty-day mortality in SOTr with bacteremia was 3% and did not differ by SOT type. CONCLUSIONS Almost 1/10 SOTr may develop bacteremia during the first year post-transplant associated with low mortality. Lower bacteremia rates have been observed since 2014 and in patients receiving cotrimoxazole prophylaxis. Variabilities in incidence, timing, and pathogen of bacteremia across different SOT types may be used to tailor prophylactic and clinical approaches

Chronologically dating the early assembly of the Milky Way

The standard cosmological model predicts that galaxies are built through hierarchical assembly on cosmological timescales1,2. The Milky Way, like other disk galaxies, underwent violent mergers and accretion of small satellite galaxies in its early history. Owing to Gaia Data Release 23 and spectroscopic surveys4, the stellar remnants of such mergers have been identified5,6,7. The chronological dating of such events is crucial to uncover the formation and evolution of the Galaxy at high redshift, but it has so far been challenging due to difficulties in obtaining precise ages for these oldest stars. Here we combine asteroseismology—the study of stellar oscillations—with kinematics and chemical abundances to estimate precise stellar ages (~11%) for a sample of stars observed by the Kepler space mission8. Crucially, this sample includes not only some of the oldest stars that were formed inside the Galaxy but also stars formed externally and subsequently accreted onto the Milky Way. Leveraging this resolution in age, we provide compelling evidence in favour of models in which the Galaxy had already formed a substantial population of its stars (which now reside mainly in its thick disk) before the infall of the satellite galaxy Gaia-Enceladus/Sausage5,6 around 10 billion years ago

A Decade of Genetic Counseling in Frontotemporal Dementia Affected Families: Few Counseling Requests and much Familial Opposition to Testing

A decade of genetic counseling of frontotemporal dementia (FTD) affected families has generated two important observations. First, the uptake rate for presymptomatic testing for FTD is low in our department of Clinical Genetics at the Erasmus Medical Center in the Netherlands. Second, FTD at-risk counselees reported substantial familial opposition to genetic testing, which is distinct from the attitude in Huntington Disease affected families. We hypothesize that the low acceptance for FTD genetic counseling is consequential to the familial opposition and explain this within the theoretical framework of separation-individuation. Furthermore, we hypothesize that separation-individuation problems do not similarly influence the acceptance of HD genetic counseling, due to the educative role of the well-organised patient organization for HD in the Netherlands. We offer counseling recommendations that serve to facilitate the individuation of the counselee with respect to the FTD genetic test

Estudio geomorfológico y paleoambiental de las avalanchas de escombros de Maca y Lari, Valle de Colca

El Valle del Colca, sur de Perú, es una zona geológicamente activa, afectada por la ocurrencia de deslizamientos. En este estudio nos centramos en la estratigrafía de los sedimentos desplazados por los movimientos de masas de Maca y Lari. El Río Colca va socavando constantemente una secuencia de sedimentos lacustres subyacentes a un depósito de la avalancha de escombros. Esto causa hundimiento y deformación en toda la secuencia, afectando a los pueblos asentados en la parte alta. Se ha realizado un estudio textural, estructural y estratigráfico en campo de la secuencia involucrada en los deslizamientos. La datación por 14C (radiocarbono) de los sedimentos orgánicos y el análisis paleomagnético de los sedimentos lacustres se aplicaron para restringir la edad y la relación espacial del diamicton (material detrítico con partículas de distintos tamaños) de avalancha de escombros involucrado en la deformación. Nuestros resultados preliminares indican que la avalancha de escombros de Maca es más joven que los depósitos de avalancha de escombros de Lari. El evento en Maca conserva la superficie original, no deformó significativamente los sedimentos lacustres inferiores y represó el río formando un lago. La avalancha de escombros de Lari no conserva la superficie original y está cubierta por hasta 10 m de sedimentos. Durante el emplazamiento, se rasgaron y deformaron profundamente los sedimentos lacustres subyacentes. Los sedimentos lacustres por encima y por debajo de ambas avalanchas registran magnetización de polaridad normal. Se hizo la correlación de los sedimentos lacustres debajo de las avalanchas con el subchron de Jaramillo y los sedimentos sobre las avalanchas con el Chron Brunhes. La cronoestratigrafía paleomagnética puede ayudar a limitar mejor los eventos geológicos en el Valle del Colca. La edad radiocarbono de sedimentos lacustres en la parte superior de la secuencia de Maca, indica una edad de emplazamiento de avalancha de escombros de 0.010-0.008 Ma. El deslizamiento pudo haber ocurrido en un clima húmedo y de desglaciación. Una mejor comprensión de la dinámica de emplazamiento de las paleo-avalanchas de escombros ayudará a entender los peligros actuales y futuros en el Valle del Colca

Replication and shedding kinetics of infectious hematopoietic necrosis virus in juvenile rainbow trout

Viral replication and shedding are key components of transmission and fitness, the kinetics of which are heavily dependent on virus, host, and environmental factors. To date, no studies have quantified the shedding kinetics of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss), or how they are associated with replication, making it difficult to ascertain the transmission dynamics of this pathogen of high agricultural and conservation importance. Here, the replication and shedding kinetics of two M genogroup IHNV genotypes were examined in their naturally co-evolved rainbow trout host. Within host virus replication began rapidly, approaching maximum values by day 3 post-infection, after which viral load was maintained or gradually dropped through day 7. Host innate immune response measured as stimulation of Mx-1 gene expression generally followed within host viral loads. Shedding also began very quickly and peaked within 2 days, defining a generally uniform early peak period of shedding from 1 to 4 days after exposure to virus. This was followed by a post-peak period where shedding declined, such that the majority of fish were no longer shedding by day 12 post-infection. Despite similar kinetics, the average shedding rate over the course of infection was significantly lower in mixed compared to single genotype infections, suggesting a competition effect, however, this did not significantly impact the total amount of virus shed. The data also indicated that the duration of shedding, rather than peak amount of virus shed, was correlated with fish mortality. Generally, the majority of virus produced during infection appeared to be shed into the environment rather than maintained in the host, although there was more retention of within host virus during the post-peak period. Viral virulence was correlated with shedding, such that the more virulent of the two genotypes shed more total virus. This fundamental understanding of IHNV shedding kinetics and variation at the individual fish level could assist with management decisions about how to respond to disease outbreaks when they occur. (C) 2016 Elsevier B.V. All rights reserved

Genome Wide Analysis of Acute Myeloid Leukemia Reveal Leukemia Specific Methylome and Subtype Specific Hypomethylation of Repeats

Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq) has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML) we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. Two genes (SPHKAP and DPP6) with significantly methylated promoters were of interest and further analysis of their expression showed them to be repressed in AML. We also demonstrated considerable cytogenetic subtype specificity in the methylomes affecting different genomic features. Significantly distinct patterns of hypomethylation of certain interspersed repeat elements were associated with cytogenetic subtypes. The methylation patterns of members of the SINE family tightly clustered all leukemic patients with an enrichment of Alu repeats with a high CpG density (P<0.0001). We were able to demonstrate significant inverse correlation between intragenic interspersed repeat sequence methylation and gene expression with SINEs showing the strongest inverse correlation (R2 = 0.7). We conclude that the alterations in DNA methylation that accompany the development of AML affect not only the promoters, but also the non-promoter genomic features, with significant demethylation of certain interspersed repeat DNA elements being associated with AML cytogenetic subtypes. MeDIP-seq data were validated using bisulfite pyrosequencing and the Infinium array

Perspectives on ethnic and racial disparities in Alzheimer\u27s disease and related dementias: Update and areas of immediate need

Alzheimer\u27s disease and related dementias (ADRDs) are a global crisis facing the aging population and society as a whole. With the numbers of people with ADRDs predicted to rise dramatically across the world, the scientific community can no longer neglect the need for research focusing on ADRDs among underrepresented ethnoracial diverse groups. The Alzheimer\u27s Association International Society to Advance Alzheimer\u27s Research and Treatment (ISTAART; alz.org/ISTAART) comprises a number of professional interest areas (PIAs), each focusing on a major scientific area associated with ADRDs. We leverage the expertise of the existing international cadre of ISTAART scientists and experts to synthesize a cross-PIA white paper that provides both a concise “state-of-the-science” report of ethnoracial factors across PIA foci and updated recommendations to address immediate needs to advance ADRD science across ethnoracial populations. © 2018 The Author

Impact of early enteral versus parenteral nutrition on mortality in patients requiring mechanical ventilation and catecholamines: study protocol for a randomized controlled trial (NUTRIREA-2)

BACKGROUND: Nutritional support is crucial to the management of patients receiving invasive mechanical ventilation (IMV) and the most commonly prescribed treatment in intensive care units (ICUs). International guidelines consistently indicate that enteral nutrition (EN) should be preferred over parenteral nutrition (PN) whenever possible and started as early as possible. However, no adequately designed study has evaluated whether a specific nutritional modality is associated with decreased mortality. The primary goal of this trial is to assess the hypothesis that early first-line EN, as compared to early first-line PN, decreases day 28 all-cause mortality in patients receiving IMV and vasoactive drugs for shock. METHODS/DESIGN: The NUTRIREA-2 study is a multicenter, open-label, parallel-group, randomized controlled trial comparing early PN versus early EN in critically ill patients requiring IMV for an expected duration of at least 48 hours, combined with vasoactive drugs, for shock. Patients will be allocated at random to first-line PN for at least 72 hours or to first-line EN. In both groups, nutritional support will be started within 24 hours after IMV initiation. Calorie targets will be 20 to 25 kcal/kg/day during the first week, then 25 to 30 kcal/kg/day thereafter. Patients receiving PN may be switched to EN after at least 72 hours in the event of shock resolution (no vasoactive drugs for 24 consecutive hours and arterial lactic acid level below 2 mmol/L). On day 7, all patients receiving PN and having no contraindications to EN will be switched to EN. In both groups, supplemental PN may be added to EN after day 7 in patients with persistent intolerance to EN and inadequate calorie intake. We plan to recruit 2,854 patients at 44 participating ICUs. DISCUSSION: The NUTRIREA-2 study is the first large randomized controlled trial designed to assess the hypothesis that early EN improves survival compared to early PN in ICU patients. Enrollment started on 22 March 2013 and is expected to end in November 2015. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01802099 (registered 27 February 2013)