bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parietal Peritoneum as a Novel Substitute for Middle Hepatic Vein Reconstruction During Living Donor Liver Transplantation
Authors: Hong Suk Kyun , Yi Nam-Joon , Cho Jae-Hyung , Lee Jeong-Moo , Hong Kwangpyo , Han Eui Soo , Lee Kwang-Woong , Suh Kyung-Suk 
Published: June 2020

Background.
Although autologous, cryopreserved, or artificial vascular grafts can be used as interpositional vascular substitutes for middle hepatic vein (MHV) reconstruction during living donor liver transplantation (LDLT), they are not always available, are limited in size and length, and are associated with risks of infection. This study aimed to evaluate the parietal peritoneum as a novel substitute for MHV reconstruction during LDLT.

Methods.
Prospectively collected data of 15 patients who underwent LDLT using the right liver with reconstruction of MHV using the recipients’ own parietal peritoneum graft were retrospectively reviewed.

Results.
The 1-, 2-, 3-, and 5-mo patency rates were 57.1%, 57.1%, 57.1%, and 28.6%, respectively. Among the 15 cases assessed, the most recent 6 cases showed patent graft flow until discharge with 1-, 2-, 3-, and 5-mo patency rates of 80.0%, 80.0%, 80.0%, and 20.0%, respectively. All patients survived with tolerable liver function tests. There were no significant congestion-related problems, except for 1 patient who experienced MHV thrombosis requiring aspiration thrombectomy and stent insertion. There were no infection-related complications. All patients survived to the final follow-up, with a minimum follow-up duration of 8 mo. When comparing the latter 6 cases of peritoneal grafts and the recent 28 cases of conventional polytetrafluorethylene graft, the overall patency rate of the polytetrafluorethylene group was higher (P = 0.002). There were no major differences other than long-term patency rate.

Conclusions.
Parietal peritoneum may be a novel autologous substitute for MHV reconstruction during LDLT.
Type 2 diabetes prevalence in Pakistan: what is driving this? Clues from subgroup analysis of normal weight individuals in diabetes prevalence survey of Pakistan
Authors: Aamir Azizul Hasan , Ul-Haq Zia , Fazid Sheraz , Shah Basharat Hussain , Raza Abbas , Jawa Ali , Mahar Saeed A. , Ahmad Ibrar , Qureshi Faisal Masood , Heald Adrian H. 
Published: June 2020

Background
Type 2 diabetes mellitus (T2DM) is a global health tissue. We determined factors relating to the likelihood of developing T2DM in normal BMI individuals.

Methodology
This was a cross-sectional community-based representative survey, of people aged ≥20 years in Pakistan, using HBA1c as the screening tool. The prevalence of T2DM/prediabetes in people having normal BMI together with associated risk factors was estimated.

Results
Of 6824 normal BMI individuals, there was still a high prevalence of T2DM 14.92% and in underweight at 10.14% (overall prevalence 16.96%). Corresponding rates for prediabetes for the normal BMI category: 9.79% and underweight 8.99%. Multivariate logistic regression modeling for normal BMI individuals, showed a significantly increased risk of T2DM with increasing age (odds ratio [OR] 2.1, 3.3, 4.5 and 4.8, P < 0.001 for 31–40, 41–50, 51–60 and 61 years and above respectively, compared to age decade 20–30 years). Similarly, there was a significantly high risk of T2DM with lower education level [OR for no vs graduate 2.4, 95% confidence interval (CI) 1.5–3.8]. There was a significantly increased risk of T2DM in individuals having a positive family history [OR 4.3 (95% CI 7.0–11.5)]. Overall the influence of overweight/obese on T2DM occurrence (20% increased risk) was much less than in other regions of the world.

Conclusion
There are higher than expected rates of T2DM/prediabetes in Pakistani ethnicity normal BMI individuals. Targeted screening of older individuals with historical lack of educational opportunity, with a family history of T2DM even if of normal BMI may result in a significant benefit in the Pakistan population.
An interpretable mortality prediction model for COVID-19 patients – alternative approach
Authors: Gemmar Peter 
Published: June 2020

AbstractThe pandemic spread of coronavirus leads to increased burden on healthcare services worldwide. Experience shows that required medical treatment can reach limits at local clinics and fast and secure clinical assessment of the disease severity becomes vital. In [1] a model is presented for predicting the mortality of COVID-19 patients from their biomarkers. Three biomarkers have been selected by ranking with a supervised Multi-tree XGBoost classifier. The prediction model is built up as a binary decision tree with depth three and achieves AUC scores of up to 97.84±0.37 and 95.06± 2.21 for training and external test data sets, resp.In human assessment and decision making influencing parameters usually aren’t considered as sharp numbers but rather as Fuzzy terms [2], and inferencing primarily yields Fuzzy terms or continuous grades rather than binary decisions. Therefore, I examined a Sugenotype Fuzzy classifier [3] for disease assessment and decision support. In addition, I used an artificial neural network (SOM, [4]) for selecting the biomarkers. Modelling and validation was done with the identical data base provided by [1]. With the complete training and test data sets, the Fuzzy prediction model achieves improved AUC scores of up to 98.59 or 95.12 The improvements with the Fuzzy classifier obviously become clear as physicians can interpret output grades to belong to positive or negative class more or less strongly. An extension of the Fuzzy model, which takes into account the trend in key features over time, provides excellent results with the training data, which, however, could not be finally verified due to the lack of suitable test data. The generation and training of the Fuzzy models was fully automatic and without additional adjustment with the help of ANFIS from Matlab©.
Perinatal Granulopoiesis and Risk of Pediatric Asthma
Authors: Turturice Benjamin A. , Theorell Juliana , Koenig Mary Dawn , Tussing-Humphreys Lisa , Gold Diane R. , Litonjua Augusto A. , Oken Emily , Rifas-Shiman Sheryl L. , Perkins David L. , Finn Patricia W. 
Published: June 2020

AbstractMany perinatal characteristics are associated with risk for pediatric asthma. Identification of biologic processes influenced by these characteristics could facilitate risk stratification or new therapeutic targets. Using publicly available transcriptomic data from CBMCs, transcription of genes involved in myeloid differentiation were inversely associated with pediatric asthma risk stratification based on gestational age at birth, sex, birthweight, and maternal pre-pregnancy BMI. This gene signature was validated in an independent cohort and was specifically associated with genes localizing to neutrophil specific granules. Changes in these genes correlated with changes in protein abundance in serum. CBMC serum levels of PGLYRP-1, a specific granule protein, and sIL6Rα, a membrane protein, were tested for association with pulmonary outcomes. PGLYRP-1 concentration was inversely associated with mid-childhood current asthma and early-teen FEV1/FVC×100. Thus, variation in neutrophil specific granule abundance at birth is associated with individual risk for pediatric asthma and reduced pulmonary function in adolescence.
Transcriptomic profiling of disease severity in patients with COVID-19 reveals role of blood clotting and vasculature related genes
Authors: Masood Kiran Iqbal , Mahmood Syed Faisal , Shahid Saba , Nasir Nosheen , Ghanchi Najia , Nasir Asghar , Jamil Bushra , Khanum Iffat , Razzak Safina , Kanji Akbar , Hasan Zahra 
Published: June 2020

AbstractCOVID-19 caused by SARS-CoV-2 manifests as a range of symptoms. Understanding the molecular mechanisms responsible for immuno-pathogenesis of disease is important for treatment and management of COVID-19. We examined host transcriptomes in moderate and severe COVID-19 cases with a view to identifying pathways that affect its progression. RNA extracted from whole blood of COVID-19 cases was analysed by microarray analysis. Moderate and severe cases were compared with healthy controls and differentially regulated genes (DEGs) categorized into cellular pathways.DEGs in COVID-19 cases were mostly related to host immune activation and cytokine signaling, pathogen uptake, host defenses, blood and vasculature genes, and SARS-CoV-2- and other virus-affected pathways. The DEGs in these pathways were increased in severe compared with moderate cases. In a severe COVID-19 patient with an unfavourable outcome we observed dysregulation of genes in platelet homeostasis and cardiac conduction and fibrin clotting with disease progression.COVID-19 morbidity is associated with cytokine activation, cardiovascular risk and thrombosis. We identified DEGs related to dysregulation of blood clotting and homeostasis, platelet activation pathways and to be associated with disease progression. These can be biomarkers of disease progression and also potential targets for treatment interventions in COVID-19.
Rapid inactivation of SARS-CoV-2 with LED irradiation of visible spectrum wavelenghts
Authors: De Santis R. , Luca V. , Faggioni G. , Fillo S. , Stefanelli P. , Rezza G. , Lista F. 
Published: June 2020

AbstractThe COVID-19 pandemic has caused a global health crisis. The difficulty to control the viral spread due to the absence of vaccines and prophylactics measures has raised concerns about prevention and control of SARS-CoV-2. Therefore, it becomes more and more crucial the reduction of environmental risk factors through viral inactivation of aerosols and fomites. Photodynamic inactivation of microorganisms by light energy emitted in the visible spectrum region (VIS), not harmful for mammalian cells and safe for humans, has recently been described. A LED-device emitting a special combination of frequencies in the visible light spectrum was tested on SARS-CoV-2 infected cell surnatant dilutions in order to evaluate the antiviral efficacy. This preliminary in vitro study showed for the first time the ability to inactivate SARS-CoV-2 through LED irradiation of visible spectrum wavelengths. If further and more extensive studies will confirm these data, the usage of this LED could potentially have a big impact on the sanitization of virtually all human environments.
Genetic diversity among SARS-CoV2 strains in South America may impact performance of Molecular detection
Authors: Ramírez Juan David , Muñoz Marina , Hernández Carolina , Florez Carolina , Gomez Sergio , Rico Angelica , Pardo Lisseth , Barrios Esther C. , Paniz-Mondolfi Alberto 
Published: June 2020

AbstractSince its emergence in Wuhan (China) on December 2019 the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide. After its arrival in South America in February 2020 the virus has expanded throughout the region infecting over 900,000 individuals with approximately 41,000 reported deaths to date. In response to the rapidly growing number of cases, a number of different primer-probe sets have been developed. However, despite being highly specific most of these primer-probe sets are known to exhibit variable sensitivity.Currently, there are more than 700 SARS-CoV2 whole genome sequences deposited in databases from Brazil, Chile, Ecuador, Colombia, Uruguay, Peru and Argentina. To test how regional viral diversity may impact oligo binding sites and affect test performance, we reviewed all available primer-probe sets targeting the E, N and RdRp genes against available South American SARS-CoV-2 genomes checking for nucleotide variations in annealing sites. Results from this in silico analysis showed no nucleotide variations on the E-gene target region, in contrast to the N and RdRp genes which showed massive nucleotide variations within oligo binding sites. In lines with previous data, our results suggest that E-gene stands as the most conserved and reliable target when considering single-gene target testing for molecular diagnosis of SARS-CoV-2 in South America.
Naturalistic coding of working memory in primate prefrontal cortex
Authors: Roussy Megan , Luna Rogelio , Duong Lyndon , Corrigan Benjamin , Gulli Roberto A. , Nogueira Ramon , Moreno-Bote Ruben , Sachs Adam J. , Palaniyappan Lena , Martinez-Trujillo Julio C. 
Published: June 2020

SummaryThe primate lateral prefrontal cortex (LPFC) is considered fundamental for temporarily maintaining and manipulating mental representations that serve behavior, a cognitive function known as working memory1. Studies in non-human primates have shown that LPFC lesions impair working memory2and that LPFC neuronal activity encodes working memory representations3. However, such studies have used simple displays and constrained gaze while subjects held information in working memory3, which put into question their ethological validity4,5. Currently, it remains unclear whether LPFC microcircuits can support working memory function during natural behavior. We tested macaque monkeys in a working memory navigation task in a life-like virtual environment while their gaze was unconstrained. We show that LPFC neuronal populations robustly encode working memory representations in these conditions. Furthermore, low doses of the NMDA receptor antagonist, ketamine, impaired working memory performance while sparing perceptual and motor skills. Ketamine decreased the firing of narrow spiking inhibitory interneurons and increased the firing of broad spiking cells reducing population decoding accuracy for remembered locations. Our results show that primate LPFC generates robust neural codes for working memory in naturalistic settings and that such codes rely upon a fine balance between the activation of excitatory and inhibitory neurons.
Machine Learning to Predict Neonatal Mortality Using Public Health Data from São Paulo - Brazil
Authors: Beluzo Carlos Eduardo , Alves Luciana Correia , Silva Everton , Bresan Rodrigo , Arruda Natália , Carvalho Tiago 
Published: June 2020

AbstractInfant mortality is one of the most important socioeconomic and health quality indicators in the world. In Brazil, neonatal mortality accounts to 70% of the infant mortality. Despite its importance, neonatal mortality shows increasing signals, which causes concerns about the necessity of efficient and effective methods able to help reducing it. In this paper a new approach is proposed to classify newborns that may be susceptible to neonatal mortality by applying supervised machine learning methods on public health features. The approach is evaluated in a sample of 15,858 records extracted from SPNeoDeath dataset, which were created on this paper, from SINASC and SIM databases from São Paulo city (Brazil) for this paper intent. As a results an average AUC of 0.96 was achieved in classifying samples as susceptible to death or not with SVM, XGBoost, Logistic Regression and Random Forests machine learning algorithms. Furthermore the SHAP method was used to understand the features that mostly influenced the algorithms output.
Low-cost measurement of facemask efficacy for filtering expelled droplets during speech
Authors: Fischer Emma P. , Fischer Martin C. , Grass David , Henrion Isaac , Warren Warren S. , Westman Eric 
Published: June 2020

AbstractMandates for mask use in public during the recent COVID-19 pandemic, worsened by global shortage of commercial supplies, have led to widespread use of homemade masks and mask alternatives. It is assumed that wearing such masks reduces the likelihood for an infected person to spread the disease, but many of these mask designs have not been tested in practice. We have applied a simple optical measurement method to evaluate the efficacy of masks to reduce the transmission of respiratory droplets during regular speech. We compare a variety of commonly available mask types and observe that some mask types approach the performance of standard surgical masks, while some mask alternatives, such as neck fleece or bandanas, offer very little protection. Our measurement setup is inexpensive and can be built and operated by non-experts, allowing for rapid evaluation of mask performance during speech, sneezing, or coughing.
Nationwide incidence of sarcomas and connective tissue tumors of intermediate malignancy over four years using an expert pathology review network
Authors: de Pinieux Gonzague , Karanian-Philippe Marie , Loarer Francois Le , Guellec Sophie Le , Chabaud Sylvie , Terrier Philippe , Bouvier Corinne , Battistella Maxime , Neuville Agnès , Robin Yves-Marie , Emile Jean-Francois , Moreau Anne , Larousserie Frederique , Leroux Agnes , Stock Nathalie , Lae Marick , Collin Francoise , Weinbreck Nicolas , Aubert Sebastien , Mishellany Florence , Charon-Barra Céline , Croce Sabrina , Doucet Laurent , Quintin-Rouet Isabelle , Chateau Marie-Christine , Bazille Celine , Valo Isabelle , Chetaille Bruno , Ortonne Nicolas , Gomez-Brouchet Anne , Rochaix Philippe , Muret Anne De , Ghnassia Jean-Pierre , Mescam-Mancini Lenaig , Macagno Nicolas , Birtwisle-Peyrottes Isabelle , Delfour Christophe , Angot Emilie , Pommepuy Isabelle , Ranchere-Vince Dominique , Chemin-Airiau Claire , Jean-Denis Myriam , Fayet Yohan , Courrèges Jean-Baptiste , Mesli Nouria , Berchoud Juliane , Toulmonde Maud , Italiano Antoine , Cesne Axel Le , Penel Nicolas , Ducimetiere Francoise , Gouin Francois , Coindre Jean-Michel , Blay Jean-Yves 
Published: June 2020

AbstractBackgroundSince 2010, NETSARC and RREPS collected and reviewed prospectively all cases of sarcomas and tumors of intermediate malignancy (TIM) nationwide.MethodsThe nationwide incidence of sarcoma or TIM (2013-2016), confirmed by expert pathologists using WHO classification are presented. Yearly variations and correlation with published clinical trials was analyzed.Results139 histological subtypes are reported among the 25172 patients with sarcomas (n=18710, 64%) or TIM (n=6460, 36%), respectively n=5838, n=6153, n=6654, and n=6527 yearly from 2013 to 2016. Over these 4 years, the yearly incidence of sarcomas and TIM was therefore 79.7, 24.9 and 95.1/106/year, above that previously reported. GIST, liposarcoma, leiomyosarcomas, undifferentiated sarcomas represented 13%, 13%, 11% and 11% of tumors. Only GIST, as a single entity had a yearly incidence above 10/million/year. There were respectively 30, 63 and 66 different histological subtypes of sarcomas or TIM with an incidence ranging from 10 to 1/106, 1-0.1/106, or < 0.1/106/year respectively. The 2 later “incidence groups” included 21% of the patients. The incidence of 8 histotypes varied significantly over this 4 years. Patients with tumors with an incidence above 1/106per year have significantly higher numbers of dedicated published phase III and phase II clinical trials (p<10−6).ConclusionsThis nationwide registry of sarcoma patients with histology reviewed by sarcoma experts shows that the incidence of sarcoma and TIM is higher than reported, and that tumors with an incidence<106/year have a much lower access to clinical trials.
A path towards SARS-CoV-2 attenuation: metabolic pressure on CTP synthesis rules the virus evolution
Authors: Ou Zhihua , Ouzounis Christos , Wang Daxi , Sun Wanying , Li Junhua , Chen Weijun , Marlière Philippe , Danchin Antoine 
Published: June 2020

ABSTRACTFighting the COVID-19 epidemic summons deep understanding of the way SARS-CoV-2 taps into its host cell metabolic resources. We describe here the singular metabolic background that creates a bottleneck constraining coronaviruses to evolve towards likely attenuation in the long term. Cytidine triphosphate (CTP) is at the crossroad of the biosynthetic processes that allow the virus to multiply. This is because CTP is in demand for three essential steps. It is a building block of the virus genome, it is required for synthesis of the cytosine-based liponucleotide precursors of the viral envelope and, finally, it is a critical building block of the host transfer RNAs synthesis. The CCA 3’-end of all the transfer RNAs required to translate the RNA genome and further transcripts into the proteins used to build active virus copies is not coded in the human genome. It must be synthesized de novo from CTP and ATP. Furthermore, intermediary metabolism is built on compulsory steps of synthesis and salvage of cytosine-based metabolites via uridine triphosphate (UTP) that keep limiting CTP availability. As a consequence, accidental replication errors tend to replace cytosine by uracil in the genome, unless recombination events allow the sequence to return to its ancestral sequences. We document some of the consequences of this situation in the function of viral proteins. We also highlight and provide araison d’êtreto viperin, an enzyme of innate antiviral immunity, which synthesizes 3’-deoxy-3′,4’-didehydro-CTP (ddhCTP) as an extremely efficient antiviral nucleotide.
Detection of hard and soft selective sweeps fromDrosophila melanogasterpopulation genomic data
Authors: Garud Nandita , Messer Philipp W. , Petrov Dmitri 
Published: June 2020

AbstractWhether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population ofDrosophila melanogaster(DGRP) allowed us to rediscover three known cases of adaptation at the lociAce,Cyp6g1, andCHKov1known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harriset al.2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim, confusingly, that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps inD. melanogasterare first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that the demographic models employed in such analyses are generally necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require fitting a very large number of free parameters.
Comparison of COVID-19 case and death counts in the United States reported by four online trackers: January 22-May 31, 2020
Authors: Smith Jinkinson 
Published: June 2020

AbstractThe first purpose of this study is to describe a project focused on comparing the numbers of COVID-19 cases and deaths in the United States reported by four different online trackers, namely, those maintained by USAFacts, the New York Times, Johns Hopkins University, and the COVID Tracking Project. The second purpose of this study is to present results from the first five months of 2020 (January 22-May 31, 2020). This project is ongoing, so it will be updated regularly as new data from each of these trackers become available. Based on the time period included, the NYT has reported more cases than any of the other three trackers since late March/early April, and COVID Tracking Project has reported fewer deaths than any of the other three trackers since mid-March. It is hoped that the discrepancies identified by this project will provide avenues for research on their causes.