bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma galectin-9 as a predictor of adverse non-AIDS events in persons with chronic HIV during suppressive antiretroviral therapy
Authors: Premeaux Thomas A. , Moser Carlee B. , McKhann Ashley , Hoenigl Martin , Laws Elizabeth I. , Aquino Draven L. , Lederman Michael M. , Landay Alan L. , Gianella Sara , Ndhlovu Lishomwa C. 
Published: August 2021

Background:
People with HIV (PWH) on antiretroviral therapy (ART) still experience an increased risk of morbidity and mortality, presumably driven by chronic inflammation, yet predictors of discrete or combinatorial outcomes remain unclear. Galectin-9 (Gal-9), a driver of both inflammatory and immunosuppressive responses, has been associated with HIV disease progression and multimorbidity.

Objective:
To determine whether plasma Gal-9 levels are associated with the occurrence of specific non-AIDS events (NAEs) in PWH initiating ART.

Design:
We performed a nested case–control study of PWH enrolled from 2001 to 2009 and evaluated pre-ART (66 cases, 97 controls), a year post-ART (112 cases, 211 controls), and immediately preceding an event (89 cases, 162 controls). Events included myocardial infarction/stroke, malignancy, serious bacterial infection, or death.

Methods:
Plasma Gal-9 levels were assessed by ELISA. Conditional logistic regression assessed associations with NAEs and Spearman's correlations compared Gal-9 with other previously assessed biomarkers.

Results:
NAEs occurred at a median of 2.8 years (1.7–4.6) after ART initiation. Higher Gal-9 levels were associated with increased risk of NAEs at year 1 and preevent [odds ratio (OR) per 1 interquartile range = 1.4–1.6; all P < 0.05], specifically myocardial infarction/stroke at year 1 (OR = 1.9; P = 0.029). Gal-9 also correlated with multiple inflammatory and immune activation predictors of NAEs (all timepoints).

Conclusion:
Elevated Gal-9 levels are predictive of deleterious NAEs, particularly cardiovascular complications. Whether the Gal-9 pathway, potentially binding to its putative ligands, is active in the pathogenesis of these outcomes warrants further investigation to determine if targeting Gal-9 may slow or reverse the risk of NAEs.
Conversion to Open Surgery in Laparoscopic Colorectal Cancer Resection: Predictive Factors and its Impact on Long-Term Outcomes. A Case Series Study
Authors: Baixauli Jorge , Cienfuegos Javier A. , Martinez Regueira Fernando , Pastor Carlos , Justicia Carlos S. , Valentí Víctor , Rotellar Fernando , Hernández Lizoáin José L. 
Published: August 2021

Background:
Laparoscopic resection is the treatment of choice for colorectal cancer. Rates of conversion to open surgery range between 7% and 30% and controversy exists as to the effect of this on oncologic outcomes. The objective of this study was to analyze what factors are predictive of conversion and what effect they have on oncologic outcomes.

Methods:
From a prospective database of patients undergoing laparoscopic surgery between 2000 and 2018 a univariate and multivariate analyses were made of demographic, pathologic, and surgical variables together with complementary treatments comparing purely laparoscopic resection with conversions to open surgery. Overall and disease-free survival were compared using the Kaplan-Meier method.

Results:
Of a total of 829 patients, 43 (5.18%) converted to open surgery. In the univariate analysis, 12 variables were significantly associated with conversion, of which left-sided resection [odds ratio (OR): 2.908; P=0.02], resection of the rectum (OR: 4.749, P=0.014), and local invasion of the tumor (OR: 6.905, P<0.01) were independently predictive factors in the multiple logistic regression. Female sex was associated with fewer conversions (OR: 0.375, P=0.012). The incidence and pattern of relapses were similar in both groups and there were no significant differences between overall and disease-free survival.

Conclusions:
Left-sided resections, resections of the rectum and tumor invasion of neighboring structures are associated with higher rates of conversion. Female sex is associated with fewer conversions. Conversion to open surgery does not compromise oncologic outcomes at 5 and 10 years.
The Value of Preoperative Ultrasound in the Detection of Contralateral Occult Inguinal Hernia in the Treatment of Symptomatic Inguinal Hernia
Authors: Ozgur Ilker , Karatas Irem , Bozkurt Halil A. , Keskin Metin , Akyuz Ali 
Published: August 2021

Background:
The true incidence of contralateral occult inguinal hernia (OIH) is a debate. The repair of contralateral OIH in the treatment context of clinical symptomatic unilateral inguinal hernia (IH) is controversial. This study aimed to assess the effect and clinical benefit of preoperative ultrasound (US) in the diagnosis of contralateral OIH performed before surgery.

Methods:
The retrospective data of 155 consecutive male patients who underwent IH repair between January 2014 and January 2020 were analyzed. The surgical procedures for IH and the clinical outcomes of the US were evaluated.

Results:
Of 155 patients, 29 (18.7%) presented with bilateral IH. Preoperative US was performed in 73 cases of clinical unilateral IH (n=126), and 30 (23.8%) patients were found to have a contralateral OIH. The totally extrapreperitoneal (TEP) or Lichtenstein repair was conducted. Bilateral IH repair was proposed for all, but only 28 agreed and underwent bilateral repair. Patients with clinically bilateral hernia had more complications compared with patients diagnosed to have occult contralateral IH after the US (n=3 vs. n=0). In the overall group, the TEP procedure resulted in shorter hospital stay (P=0.001) and less pain (P=0.021).

Conclusions:
The preoperative US may be recommended to assess the presence of a contralateral OIH as it is a noninvasive, radiation-free, widely available, relatively cheap diagnostic method. The preoperative US may change the surgical approach in up to 1/4 patients with a clinical unilateral IH. Either Lichtenstein repair or TEP repair can be performed with an acceptable complication rate in the case of OIH.
Useful Technique for Creating a Good Liver Parenchymal Visual Transection Plane During Laparoscopic Partial Hepatectomy
Authors: Kawasaki Yota , Iino Satoshi , Yamasaki Yoichi , Hozaka Yuto , Idichi Tetsuya , Kurahara Hiroshi , Mataki Yuko , Ueno Shinichi , Ohtsuka Takao 
Published: August 2021

Background:
Creating a good surgical visual field is one of the most important factors for performing a successful surgery. Here, we introduce a useful technique for creating a good liver parenchymal visual transection plane during laparoscopic partial hepatectomy and compare the perioperative outcomes of our current technique with those of conventional techniques.

Methods:
We reviewed the data of patients who underwent laparoscopic partial hepatectomy between July 2016 and December 2020. The current technique for creating transection planes was first applied in our department in April 2019. The patients were divided into conventional (forceps) and current (silicone ring) technique groups, depending on the surgical technique.

Results:
Twenty-eight and 12 patients underwent laparoscopic partial hepatectomy using the conventional and current techniques, respectively, when the difficulty level—as determined by IWATE criteria—was low. Although the tumor size was significantly larger (median: 22.5 vs. 15 mm, P=0.04) in the current technique group, the estimated intraoperative blood loss was significantly lower (median: 50 vs. 100 mL, P=0.01), and the median surgical margin was significantly longer (median: 7 vs. 3 mm, P=0.02). There were no significant between-group differences in surgical time (median: 344 vs. 240 min, P=0.14), postoperative hospital stay duration (median: 11 vs. 9.5 d, P=0.051), and the incidence of complications (P=0.63).

Conclusion:
We believe that the technique involving the use of a silicone ring can result in better surgical outcomes as it provides a good visual hepatic transection plane during laparoscopic partial hepatectomy.
Searching for a “Brain Signature” of Neurodevelopmental Disorders: Event-Related Potentials and the Quest for Biomarkers of Cognition
Authors: Key Alexandra P. 
Published: August 2021

Summary:This review summarizes main applications of event-related potentials (ERPs) to the study of cognitive processes in persons with neurodevelopmental disorders, for whom traditional behavioral assessments may not be suitable. A brief introduction to the ERPs is followed by a review of empirical studies using passive ERP paradigms to address three main questions: characterizing individual differences, predicting risk for poor developmental outcomes, and documenting treatment effects in persons with neurodevelopmental disorders. Evidence across studies reveals feasibility of ERP methodology in a wide range of clinical populations and notes consistently stronger brain–behavior associations involving ERP measures of higher-order cognition compared with sensory–perceptual processes. The final section describes the current limitations of ERP methodology that need to be addressed before it could be used as a clinical tool and highlights the needed steps toward translating ERPs from group-level research applications to individually interpretable clinical use.
Assessing unused residual Pfizer-BioNTech COVID-19 vaccine: a community observational study
Authors: Hubbard Stephen , Bais Rajlaxmi 
Published: August 2021

SummaryWorldwide morbidity and mortality associated with Covid-19 are severe and ongoing. The Pfizer-BioNTech vaccine is said to be up to 95% effective against severe disease or death. We were able to demonstrate that an additional 9.8% of COVID-19 vaccine doses could theoretically be given if the residual vaccine within the reconstituted Pfizer vials after six doses are extracted were used. This could be achieved by aseptically combining this excess vaccine from multiple vials to achieve full 0.3ml doses.MethodsAn observational study was conducted in April, 2021, at a mass vaccine site run by a community volunteer organization on Bainbridge Island, Washington. We measured the amount of Pfizer-BioNTech COVID-19 vaccine that was left in 172 vials after six doses had been withdrawn per Centers for Disease Control (CDC) protocol.ResultsA total of 30.68 ml of leftover vaccine was measured and discarded as medical waste. 1,036 doses were given from these vials. An extra 102 doses theoretically could have been given using the residual vaccine in the vials. This would have resulted in 9.8% additional doses of COVID-19 vaccine without requiring new vials.ConclusionThe ability to combine solution from reconstituted Pfizer vaccine vials to minimize waste and obtain additional doses of vaccine could result in an increase in the number of individuals that could be vaccinated worldwide without additional cost. Further studies to validate our findings are warranted. Clinical trials to study the feasibility, safety and efficacy of protocols using this excess vaccine should be considered.
Rapid expansion of SARS-CoV-2 variants of concern is a result of adaptive epistasis
Authors: Garvin Michael R. , Prates Erica T. , Romero Jonathon , Cliff Ashley , Machado Gazolla Joao Gabriel Felipe , Pickholz Monica , Pavicic Mirko , Jacobson Daniel 
Published: August 2021

AbstractThe SARS-CoV-2 pandemic recently entered an alarming new phase with the emergence of the variants of concern (VOC) and understanding their biology is paramount to predicting future ones. Current efforts mainly focus on mutations in the spike glycoprotein (S), but changes in other regions of the viral proteome are likely key. We analyzed more than 900,000 SARS-CoV-2 genomes with a computational systems biology approach including a haplotype network and protein structural analyses to reveal lineage-defining mutations and their critical functional attributes. Our results indicate that increased transmission is promoted by epistasis, i.e., combinations of mutations in S and other viral proteins. Mutations in the non-S proteins involve immune-antagonism and replication performance, suggesting convergent evolution. Furthermore, adaptive mutations appear in geographically disparate locations, suggesting that either independent, repeat mutation events or recombination among different strains are generating VOC. We demonstrate that recombination is a stronger hypothesis, and may be accelerating the emergence of VOC by bringing together cooperative mutations. This emphasizes the importance of a global response to stop the COVID-19 pandemic.
MFDNN: Multi-channel feature deep neural network algorithm to identify Covid19 chest X-ray images
Authors: Pan Liangrui , Ji Boya , Wang Xiaoqi , Peng Shaolaing 
Published: August 2021

AbstractThe use of chest X-ray images (CXI) to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) caused by Coronavirus Disease 2019 (COVID-19) is life-saving important for both patients and doctors. This research proposed a multi-channel feature deep neural network algorithm to screen people infected with COVID-19. The algorithm integrates data oversampling technology and a multi-channel feature deep neural network model to carry out the training process in an end-to-end manner. In the experiment, we used a publicly available CXI database with 10,192 Normal, 6012 Lung Opacity (Non-COVID lung infection), and 1345 Viral Pneumonia images. Compared with traditional deep learning models (Densenet201, ResNet50, VGG19, GoogLeNet), the MFDNN model obtains an average test accuracy of 93.19% in all data. Furthermore, in each type of screening, the precision, recall, and F1 Score of the MFDNN model are also better than traditional deep learning networks. Secondly, compared with the latest CoroDet model, the MFDNN algorithm is 1.91% higher than the CoroDet model in the experiment of detecting the four categories of COVID19 infected persons. Finally, our experimental code will be placed at https://github.com/panliangrui/covid19.
Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy
Authors: Parikh Victoria N. , Ioannidis Alexander G. , Jimenez-Morales David , Gorzynski John E. , De Jong Hannah N. , Liu Xiran , Roque Jonasel , Cepeda-Espinoza Victoria P. , Osoegawa Kazutoyo , Hughes Chris , Sutton Shirley C. , Youlton Nathan , Joshi Ruchi , Amar David , Tanigawa Yosuke , Russo Douglas , Wong Justin , Lauzon Jessie T. , Edelson Jacob , Montserrat Daniel Mas , Kwon Yongchan , Rubinacci Simone , Delaneau Olivier , Cappello Lorenzo , Kim Jaehee , Shoura Massa J. , Raja Archana N. , Watson Nathaniel , Hammond Nathan , Spiteri Elizabeth , Mallempati Kalyan C. , Montero-Martín Gonzalo , Christle Jeffrey , Kim Jennifer , Kirillova Anna , Seo Kinya , Huang Yong , Zhao Chunli , Moreno-Grau Sonia , Hershman Steven G. , Dalton Karen P. , Zhen Jimmy , Kamm Jack , Bhatt Karan D. , Isakova Alina , Morri Maurizio , Ranganath Thanmayi , Blish Catherine A. , Rogers Angela J. , Nadeau Kari , Yang Samuel , Blomkalns Andra , O’Hara Ruth , Neff Norma F. , DeBoever Christopher , Szalma Sándor , Wheeler Matthew T. , Farh Kyle , Schroth Gary P. , Febbo Phil , deSouza Francis , Fernandez-Vina Marcelo , Kistler Amy , Palacios Julia , Pinsky Benjamin A. , Bustamante Carlos D. , Rivas Manuel A , Ashley Euan A. 
Published: August 2021

ABSTRACTThe SARS-CoV-2 pandemic has differentially impacted populations of varied race, ethnicity and socioeconomic status. Admixture mapping and local ancestry inference represent powerful tools to examine genetic risk within multi-ancestry genomes independent of these confounding social constructs. Here, we leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from 1,327 nasopharyngeal swab residuals and integrate them with digital phenotypes from electronic health records. We demonstrate over-representation of individuals possessing Oceanian and Indigenous American ancestry in SARS-CoV-2 positive populations. Genome-wide-association disaggregated by admixture mapping reveals regions of chromosomes 5 and 14 associated with COVID19 severity within African and Oceanic local ancestries, respectively, independent of overall ancestry fraction. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. We further present summary data from a multi-omic investigation of human-leukocyte-antigen (HLA) typing, nasopharyngeal microbiome and human transcriptomics that reveal metagenomic and HLA associations with severe COVID19 infection. This work demonstrates the power of multi-omic pandemic tracking and genomic analyses to reveal distinct epidemiologic, genetic and biological associations for those at the highest risk.
INDI – Integrated Nanobody Database for Immunoinformatics
Authors: Deszyński Piotr , Młokosiewicz Jakub , Volanakis Adam , Jaszczyszyn Igor , Castellana Natalie , Bonissone Stefano , Ganesan Rajkumar , Krawczyk Konrad 
Published: August 2021

AbstractNanobodies, a subclass of antibodies found in camelids, are a versatile molecular binding scaffold composed of a single polypeptide chain. The small size of nanobodies bestows multiple therapeutic advantages (stability, tumor penetration) with the first therapeutic approval in 2018 cementing the clinical viability of this format. Structured data and sequence information of nanobodies will enable the accelerated clinical development of nanobody-based therapeutics. Though the nanobody sequence and structure data are deposited in the public domain at an accelerating pace, the heterogeneity of sources and lack of standardization hampers reliable harvesting of nanobody information. We address this issue by creating the Integrated Database of Nanobodies for Immunoinformatics (INDI, http://research.naturalantibody.com/nanobodies). INDI collates nanobodies from all the major public outlets of biological sequences: patents, GenBank, next-generation sequencing repositories, structures and scientific publications. We equip INDI with powerful nanobody-specific sequence and text search facilitating access to more than 11 million nanobody sequences. INDI should facilitate development of novel nanobody-specific computational protocols helping to deliver on the therapeutic promise of this drug format.
Prevalence and Factors Associated with Behavioural Problems in 5-year-old Children Born with Cleft Lip and/or Palate from the Cleft Collective
Authors: Berman Samantha , Sharp Gemma C , Lewis Sarah J , Blakey Rachel , Davies Amy , Humphries Kerry , Wren Yvonne , Sandy Jonathan R , Stergiakouli Evie 
Published: August 2021

AbstractObjectivesWe determined the prevalence of behavioural problems in 5-year-old children born with Cleft Lip and/or Palate (CL/P) and compared it to the prevalence in general population samples. We also identified risk factors for behavioural problems in children with CL/P.DesignObservational study using questionnaire data from the Cleft Collective (CC) 5-Year-Old cohort study and three general population samples.Main Outcome MeasureThe Strengths and Difficulties Questionnaire (SDQ) was used to measure behavioural problems.ParticipantsA total of 340 children born with CL/P whose mothers had completed the SDQ when their child was 5 years old. Published estimates from three large cohorts were used to approximate general population SDQ scores in the UK and these were used as comparison groups; Millennium Cohort Study (MCS) (n=12,511), Office of National Statistics (ONS) normative school-age SDQ data (n=5,855) and the Avon Longitudinal Study of Parents and Children (ALSPAC) (n=9,386).ResultsAn estimated 14.3% of 5-year-old children born with CL/P experienced behavioural problems. There was strong evidence to suggest children with CL/P were more likely to experience difficulties than children in the general population, as measured by SDQ total difficulties scores from all three population cohorts: MCS (OR = 2.07 [95% CI = 1.50-2.85]; P<.001), ONS Norms (OR = 1.53 [95% CI = 1.12-2.11]; P=.008), and ALSPAC (OR = 2.37 [95% CI = 1.72-3.27]; P<.001). The odds of hyperactivity, emotional, prosocial and peer problems were increased among children in the Cleft Collective compared with children in the Millennium Cohort Study. Odds ratios and 95% confidence intervals indicated that children in the Cleft Collective were nearly twice as likely as those in the MCS (OR = 1.91 [95% CI = 1.38-2.65]; P<.001) and three times those in ALSPAC (OR = 3.20 [95% CI = 2.29-4.47]; P<.001) to experience emotional difficulties. The odds of emotional difficulties were higher in boys than girls. Maternal smoking, marital status, younger maternal age at conception, lower maternal education, receiving income support, and measures of poor maternal and familial health showed some evidence of association with behavioural problems in 5-year-old children born with CL/P.ConclusionsOur findings suggest elevated levels of behavioural problems in children born with CL/P, particularly emotional difficulties in boys, compared to the general population and indicate several factors associated observationally with these difficulties.
Accelerometer-Derived and Genetically Inferred Physical Activity and Human Disease
Authors: Khurshid Shaan , Weng Lu-Chen , Nauffal Victor , Pirruccello James P. , Venn Rachael A. , Al-Alusi Mostafa A. , Benjamin Emelia J. , Ellinor Patrick T. , Lubitz Steven A. 
Published: August 2021

AbstractPhysical activity is favorable to health but the relations with human disease and causal effects are poorly quantified. Previous studies have largely relied on self-reported estimates1–3 which are subject to recall bias, confounding, and reverse causality. Using wrist-worn accelerometer measurements from the UK Biobank, we tested associations between moderate-to-vigorous physical activity (MVPA) – both total MVPA minutes and whether MVPA was above a guideline-based threshold of ≥150 minutes/week4–6 – and incidence of over 1,200 diseases. In 96,466 adults who wore accelerometers for one week (mean age 62±8 years), MVPA was associated with 401 (33%) tested diseases at a false discovery rate of 1% during a median of 6.2 years follow-up. Greater MVPA was overwhelmingly associated with reduced disease risk (98% of associations) with hazard ratios (HRs) ranging from 0.10-0.95 per standard deviation (SD) and associations spanning all 18 disease categories tested. A similar pattern of associations was observed when assessing the guideline-based threshold of ≥150 MVPA minutes/week. We examined a polygenic risk score for MVPA as an instrumental variable for activity within a separate UK Biobank sample (N=392,058, mean age 57±8 years). Greater genetically inferred MVPA was associated with reduced risk of 182 (14%) incident diseases (HR range 0.74-0.97 per 1 SD), and included strong associations conferring reduced risks of obstructive bronchitis, peripheral vascular disease, type 2 diabetes, and gastritis/duodenitis. Objective physical activity is broadly associated with lower disease incidence and many associations are consistent with a causal effect.