bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cerebrospinal Fluid Viral Load Across the Spectrum of Untreated Human Immunodeficiency Virus Type 1 (HIV-1) Infection: A Cross-Sectional Multicenter Study
Authors: Ulfhammer Gustaf , Edén Arvid , Antinori Andrea , Brew Bruce J , Calcagno Andrea , Cinque Paola , De Zan Valentina , Hagberg Lars , Lin Amy , Nilsson Staffan , Oprea Cristiana , Pinnetti Carmela , Spudich Serena , Trunfio Mattia , Winston Alan , Price Richard W , Gisslén Magnus 
Published: November 2021

Abstract

Background
The aim of this large multicenter study was to determine variations in cerebrospinal fluid (CSF) HIV-RNA in different phases of untreated human immunodeficiency virus type 1 (HIV-1) infection and its associations with plasma HIV-RNA and other biomarkers.

Methods
Treatment naive adults with available CSF HIV-RNA quantification were included and divided into groups representing significant disease phases. Plasma HIV-RNA, CSF white blood cell count (WBC), neopterin, and albumin ratio were included when available.

Results
In total, 1018 patients were included. CSF HIV-RNA was in median (interquartile range [IQR]) 1.03 log10 (0.37–1.86) copies/mL lower than in plasma, and correlated with plasma HIV-RNA (r = 0.44, P &lt; .01), neopterin concentration in CSF (r = 0.49, P &lt; .01) and in serum (r = 0.29, P &lt; .01), CSF WBC (r = 0.34, P &lt; .01) and albumin ratio (r = 0.25, P &lt; .01). CSF HIV-RNA paralleled plasma HIV-RNA in all groups except neuroasymptomatic patients with advanced immunodeficiency (CD4 &lt; 200) and patients with HIV-associated dementia (HAD) or opportunistic central nervous system (CNS) infections. Patients with HAD had the highest CSF HIV-RNA (in median [IQR] 4.73 (3.84–5.35) log10 copies/mL). CSF &gt; plasma discordance was found in 126 of 972 individuals (13%) and varied between groups, from 1% in primary HIV, 11% in neuroasymptomatic groups, up to 30% of patients with HAD.

Conclusions
Our study confirms previous smaller observations of variations in CSF HIV-RNA in different stages of HIV disease. Overall, CSF HIV-RNA was approximately 1 log10 copies/mL lower in CSF than in plasma, but CSF discordance was found in a substantial minority of subjects, most commonly in patients with HAD, indicating increasing CNS compartmentalization paralleling disease progression.
Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection
Authors: Sundermann Alexander J , Chen Jieshi , Kumar Praveen , Ayres Ashley M , Cho Shu Ting , Ezeonwuka Chinelo , Griffith Marissa P , Miller James K , Mustapha Mustapha M , Pasculle A William , Saul Melissa I , Shutt Kathleen A , Srinivasa Vatsala , Waggle Kady , Snyder Daniel J , Cooper Vaughn S , Van Tyne Daria , Snyder Graham M , Marsh Jane W , Dubrawski Artur , Roberts Mark S , Harrison Lee H 
Published: November 2021

Abstract

Background
Most hospitals use traditional infection prevention (IP) methods for outbreak detection. We developed the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), which combines whole-genome sequencing (WGS) surveillance and machine learning (ML) of the electronic health record (EHR) to identify undetected outbreaks and the responsible transmission routes, respectively.

Methods
We performed WGS surveillance of healthcare-associated bacterial pathogens from November 2016 to November 2018. EHR ML was used to identify the transmission routes for WGS-detected outbreaks, which were investigated by an IP expert. Potential infections prevented were estimated and compared with traditional IP practice during the same period.

Results
Of 3165 isolates, there were 2752 unique patient isolates in 99 clusters involving 297 (10.8%) patient isolates identified by WGS; clusters ranged from 2–14 patients. At least 1 transmission route was detected for 65.7% of clusters. During the same time, traditional IP investigation prompted WGS for 15 suspected outbreaks involving 133 patients, for which transmission events were identified for 5 (3.8%). If EDS-HAT had been running in real time, 25–63 transmissions could have been prevented. EDS-HAT was found to be cost-saving and more effective than traditional IP practice, with overall savings of $192 408–$692 532.

Conclusions
EDS-HAT detected multiple outbreaks not identified using traditional IP methods, correctly identified the transmission routes for most outbreaks, and would save the hospital substantial costs. Traditional IP practice misidentified outbreaks for which transmission did not occur. WGS surveillance combined with EHR ML has the potential to save costs and enhance patient safety.
Minimizing the Effect of Cascade Failure in Multilayer Networks with Optimal Redistribution of Link Loads
Authors: Kumar Rajesh , Kumari Suchi , Bala Manju 
Published: November 2021

Abstract
Modern real-world infrastructure systems consist of a coupled and interdependent subsystems. These system can be modelled as interdependent multilayer networks such as communication networks, power networks, transport networks, etc. These networks are prone to cascade failure of intra-layer and inter-layer links due to overload. For example, in power distribution networks, the flow of electric current beyond their capacities may cause to fail the distribution lines. In multilayer network systems, any damage to the links (intra-layer and inter-layer) may cause cascade failure due to redistribution of loads of failed links to the live links. If it is not controlled, it may damage the entire system. However, optimally redistribution of loads of the failed links to live links can minimize the damage of live links due to overload. In this work, we propose a method to optimally redistribute loads of failed links (intra-layer and inter-layer) to the live links in the interdependent multilayer network in the event of cascade failure. For this purpose, we consider three variants of synthetic and two empirical dataset multilayer networks. Our simulation results reveal that optimal redistribution of loads reduces the number of failed links. Besides, it also reduces the amount of extra load (due to failed links) to be redistributed on the live links. It leads to enhance the number of live links and maintaining the robustness of the entire multilayer networks.
FGF10 promotes cardiac repair through a dual cellular mechanism increasing cardiomyocyte renewal and inhibiting fibrosis
Authors: Hubert Fabien , Payan Sandy M , Pelce Edeline , Bouchard Laetitia , Sturny Rachel , Lenfant Nicolas , Mottola Giovanna , Collart Frédéric , Kelly Robert G , Rochais Francesca 
Published: November 2021

Abstract

Aims
Promoting cardiomyocyte renewal represents a major therapeutic approach for heart regeneration and repair. Our study aims to investigate the relevance of FGF10 as a potential target for heart regeneration.

Methods and results
Our results first reveal that Fgf10 levels are up-regulated in the injured ventricle after MI. Adult mice with reduced Fgf10 expression subjected to MI display impaired cardiomyocyte proliferation and enhanced cardiac fibrosis, leading to a worsened cardiac function and remodelling post-MI. In contrast, conditional Fgf10 overexpression post-MI revealed that, by enhancing cardiomyocyte proliferation and preventing scar-promoting myofibroblast activation, FGF10 preserves cardiac remodelling and function. Moreover, FGF10 activates major regenerative pathways including the regulation of Meis1 expression levels, the Hippo signalling pathway and a pro-glycolytic metabolic switch. Finally, we demonstrate that elevated FGF10 levels in failing human hearts correlate with reduced fibrosis and enhanced cardiomyocyte proliferation.

Conclusions
Altogether, our study shows that FGF10 promotes cardiac regeneration and repair through two cellular mechanisms: elevating cardiomyocyte renewal and limiting fibrosis. This study thus identifies FGF10 as a clinically relevant target for heart regeneration and repair in man.
Vascular complications after transcatheter aortic valve implantation: treatment modalities and long-term clinical impact
Authors: Lunardi Mattia , Pighi Michele , Banning Adrian , Reimers Bernhard , Castriota Fausto , Tomai Fabrizio , Venturi Gabriele , Pesarini Gabriele , Scarsini Roberto , Kotronias Rafail , Regazzoli Damiano , Maurina Matteo , Nerla Roberto , De Persio Giovanni , Ribichini Flavio Luciano 
Published: November 2021

Abstract

OBJECTIVES
Vascular complications (VC) are the most frequent drawback of transcatheter aortic valve implantation (TAVI), affecting up to 20% of overall procedures. Data on the treatment and their long-term impact are scarce. The goal of this study was to report on the incidence, management and impact on the long-term outcomes of VC following TAVI.

METHODS
This was a multicentric retrospective analysis of consecutive patients undergoing TAVI. The primary endpoint was freedom from major adverse cardiac and cerebrovascular events at long-term follow-up. Adverse events were evaluated according to Valve Academic Research Consortium-2 criteria.

RESULTS
A total of 2145 patients were included: VC occurred in 188 (8.8%); of which 180 were limited to the access site. Two-thirds of the VC were minor; 8% required surgical treatment; the remaining were repaired percutaneously. The major adverse cardiac and cerebrovascular events-free survival at 2 years was 83.0% for patients with VC and 86.7% for those without (P = 0.143), but 71.9% for patients with major compared to 89.0% in those with minor VC (P = 0.022). Major VC and diabetes mellitus independently predicted worse outcomes at 2 years. The major adverse cardiac and cerebrovascular events-free survival rate and the occurrence of vascular adverse events in the long term among patients with VC at the access site treated by endovascular techniques (covered stent implantation or angioplasty) were similar to those without VC (84.2% vs 86.7%; P = 0.635).

CONCLUSIONS
Major but not minor VC impact long-term survival after TAVI. Covered stents implanted to manage VC at the access site have no impact on the long-term clinical outcome of TAVI.
Children’s and teachers’ views on digital games in the EFL classroom
Authors: Waddington Julie , Bannikova Charikova Daria 
Published: November 2021

Abstract
At a time marked by the increasing use of technology in education, the study presented in this paper explores and compares teachers’ and children’s views on the use of digital games in class. A case study is presented in a primary school setting where tablets have been fully integrated into the EFL classroom. A mixed-method approach was used to collect and analyse data from teachers and students through interviews and questionnaires. Findings are presented which compare and contrast student and teacher views on: important elements to take into account when teaching/learning English; student behaviour; affective states; and the effects of digital games on learning. Contrasting perceived positive and negative effects of using digital games, the findings support claims that more work is needed to incorporate new technologies within classroom practice in ways which foster learner-centred models and facilitate the learning and well-being of all students.
Akirin/Subolesin regulatory mechanisms at host/tick–pathogen interactions
Authors: de la Fuente José , Artigas-Jerónimo Sara , Villar Margarita 
Published: November 2021

ABSTRACTTicks and tick-borne pathogens such as Anaplasma phagocytophilum affect human and animal health worldwide and thus the characterization of host/tick–pathogen interactions is important for the control of tick-borne diseases. The vertebrate regulatory proteins Akirins and its tick ortholog, Subolesin, are conserved throughout the metazoan and involved in the regulation of different biological processes such as immune response to pathogen infection. Akirin/Subolesin have a key role in host/tick–pathogen interactions and exert its regulatory function primarily through interacting proteins such as transcription factors, chromatin remodelers and RNA-associated proteins. Recent results have provided evidence of akirin/subolesin genetic interactions and the interaction of Akirin/Subolesin with histones, thus suggesting a role in direct chromatin remodeling. Finally, and still to be proven, some models suggest the possibility of direct Akirin/Subolesin protein interactions with DNA. Future research should advance the characterization of Akirin/Subolesin interactome and its functional role at the host/tick–pathogen interface. These results have implications for translational biotechnology and medicine for the development of new effective interventions for the control of ticks and tick-borne diseases.
Coq3p relevant residues for protein activity and stability
Authors: Paulela Janaina A , Gomes Fernando , Camandona Vittoria de Lima , Alegria Thiago G P , Netto Luis E S , Bleicher Lucas , Barros Mario H , Ferreira-Junior Jose Ribamar 
Published: November 2021

Abstract
Coenzyme Q (CoQ) is an essential molecule that consists of a highly substituted benzene ring attached to a polyprenyl tail anchored in the inner mitochondrial membrane. CoQ transfers electrons from NADH dehydrogenase and succinate dehydrogenase complexes toward ubiquinol-cytochrome c reductase, and that allows aerobic growth of cells. In Saccharomyces cerevisiae, the synthesis of CoQ depends on fourteen proteins Coq1p-Co11p, Yah1p, Arh1p, and Hfd1p. Some of these proteins are components of CoQ synthome. Using ab initio molecular modeling and site-directed mutagenesis, we identified the functional residues of the O-methyltransferase Coq3p, which depends on S-adenosylmethionine for catalysis and is necessary for two O-methylation steps required for CoQ maturation. Conserved residues as well as those that coevolved in the protein structure were found to have important roles in respiratory growth, CoQ biosynthesis, and also in the stability of CoQ synthome proteins. Finally, a multiple sequence alignment showed that S. cerevisiae Coq3p has a 45 amino acid residues insertion that is poorly conserved or absent in oleaginous yeast, cells that can store up to 20% of their dry weight as lipids. These results point to the Coq3p structural determinants of its biological and catalytic function and could contribute to the development of lipid-producing yeast for biotechnology.
The pushback against state interference in science: how Lysenkoism tried to suppress Genetics and how it was eventually defeated
Authors: Ptushenko Vasily V. 
Published: November 2021

Abstract
Genetics in the Soviet Union (USSR) achieved state-of-the-art results and had reached a peak of development by the mid-1930s due to the efforts of the scientific schools of several major figures, including Sergei Navashin, Nikolai Koltsov, Grigorii Levitsky, Yuri Filipchenko, Nikolai Vavilov, and Solomon Levit. Unfortunately, the Soviet government distrusted intellectually independent science and this led to state support for a fraudulent pseudoscientific concept widely known as Lysenkoism, which hugely damaged biology as a whole. Decades of dominance of the Lysenkoism had ruinous effects and the revival of biology in the USSR in the late 1950s–early 1960s was very difficult. In fact, this was realized to be a problem for Soviet science as a whole, and many mathematicians, physicists, chemists, and other scientists made efforts to rehabilitate genetics and to transfer biology to the “jurisdiction” of science from that of politics. The key events in the history of these attempts to pushback against state interference in science, and to promote the development of genetics and molecular biology, are described in this paper. These efforts included supportive letters to the authorities (e.g., the famous “Letter of three hundred”), (re)publishing articles and giving lectures on “forbidden” science, and organizing laboratories and departments for research in genetics and molecular biology under the cover of nuclear physics or of other projects respected by the government and Communist party leaders. The result was that major figures in the hard sciences played a major part in the revival of genetics and biology in the USSR.
Peritoneal fluid progesterone and progesterone resistance in superficial endometriosis lesions
Authors: Koninckx Philippe R , Ussia Anastasia , Adamyan Leila , Gomel Victor , Martin Dan C 
Published: November 2021

Abstract
Peritoneal fluid in ovulatory women is an ovarian exudate with higher estrogen and progesterone concentrations than in plasma. In the follicular phase, progesterone concentrations are as high as plasma concentrations in the luteal phase. After ovulation, estrogen and progesterone concentrations in the peritoneal fluid are 5–10 times higher than in plasma, both in women with and without endometriosis. The histologically proliferative aspect without secretory changes of most superficial subtle lesions is not compatible with the progesterone concentrations in the peritoneal fluid. Therefore, we have to postulate a strong progesterone resistance in these lesions. The mechanism is unclear and might be a peritoneal fluid effect in women with predisposing defects in the endometrium, or isolated endometrial glands with progesterone resistance, or subtle lesions originating from the basal endometrium: the latter hypothesis is attractive since in basal endometrium progesterone does not induce secretory changes while progesterone withdrawal, not occurring in peritoneal fluid, is required to resume mitotic activity and proliferation. Hormone concentrations in the peritoneal fluid are an important factor in understanding the medical therapy of endometriosis. The effect of oestro-progestin therapy on superficial endometriosis lesions seems to be a consequence of the decreased estrogen concentrations rather than a direct progestin effect. In conclusion, the peritoneal fluid, being a secretion product of the ovarian follicule, deserves more attention in the pathophysiology and treatment of endometriosis.
Push–Pull Operators on Convex Polytopes
Authors: Kiritchenko Valentina 
Published: November 2021

AbstractA classical result of Schubert calculus is an inductive description of Schubert cycles using divided difference (or push–pull) operators in Chow rings. We define convex geometric analogs of push–pull operators and describe their applications to the theory of Newton–Okounkov convex bodies. Convex geometric push–pull operators yield an inductive construction of Newton–Okounkov polytopes of Bott–Samelson varieties. In particular, we construct a Minkowski sum of Feigin–Fourier–Littelmann–Vinberg polytopes using convex geometric push–pull operators in type $A$.
On the Joint Moments of the Characteristic Polynomials of Random Unitary Matrices
Authors: Assiotis Theodoros , Keating Jonathan P , Warren Jon 
Published: November 2021

Abstract
We establish the asymptotics of the joint moments of the characteristic polynomial of a random unitary matrix and its derivative for general real values of the exponents, proving a conjecture made by Hughes [ 40] in 2001. Moreover, we give a probabilistic representation for the leading order coefficient in the asymptotic in terms of a real-valued random variable that plays an important role in the ergodic decomposition of the Hua–Pickrell measures. This enables us to establish connections between the characteristic function of this random variable and the $\sigma $-Painlevé III’ equation.
Assessing the International Influence of Private Philanthropy: The Case of Open Society Foundations
Authors: Correa-Cabrera Guadalupe , Núñez Lucas , Ludwig Hayden 
Published: November 2021

AbstractThis article evaluates the international influence of Open Society Foundations (OSF) based on its goals and allocation of resources and takes into consideration the concerns raised by its critics. The study analyzes the objectives of this private philanthropic organization as well as its origins and the goals of its founder, George Soros. By assembling and using an original database, it also provides an overall analysis of all OSF grants assigned worldwide in the years 1999–2018 and quantitatively assesses their macro-level impact on democratic governance, freedom of expression, government accountability, and societies that promote justice and equity. Based on the available data, we find no evidence that OSF grants produce a positive impact at the macro-level on these goals nor that they effectively contribute to destabilize countries through protests and mass migrations as its critics claim. These results may have to do with lack of effectiveness or with motivations not matching the outcomes measured here. However, it is early to draw conclusions due to limited data.
Predicting Direct-Specimen SARS-CoV-2 Assay Performance Using Residual Patient Samples
Authors: Schroeder Lee F , Bachman Michael A , Idoni Allison , Gegenheimer-Holmes Jennifer , Kronick Steven L , Valdez Riccardo , Lephart Paul R 
Published: November 2021

Abstract

Background
Diagnostic sensitivities of point-of-care SARS-CoV-2 assays depend on specimen type and population-specific viral loads. Evaluation of these assays require “direct” specimens from paired-swab studies rather than more accessible residual specimens in viral transport media (VTM).

Methods
Residual VTM and limit-of-detection studies were conducted on Abbott ID NOW™ COVID-19, Quidel Sofia 2™ SARS Antigen FIA, and DiaSorin Simplexa™ COVID-19 Direct assays, with cycle threshold (CT) adjustments to approximate direct-specimen testing based on gene-target doubling each PCR cycle. Logistic regression was used to model assay performance by specimen CT. These models were applied to CT distributions of symptomatic and asymptomatic populations presenting to emergency services to predict the percentage of specimens that would be detected by each assay. A 96-sample paired-swab study was conducted to confirm model results.

Results
When using direct nasopharyngeal samples and fit with either VTM or limit-of-detection data, percent positivities for ID NOW (symptomatic 94.9%/97.4%; asymptomatic 88.4.0%/89.6%) and Simplexa (symptomatic 97.8%/97.2%; asymptomatic 91.1%/90.8%) were predicted to be similar. Likewise, percent positivities for ID NOW with direct nasal specimens (symptomatic 77.8%; asymptomatic 64.5%) and, fit with VTM data, Sofia 2 with direct nasopharyngeal specimens (symptomatic 76.6%, asymptomatic 60.3%) were similar. The paired-swab study comparing direct nasopharyngeal specimens on ID NOW and nasopharyngeal VTM specimens on Simplexa showed 99% concordance.

Conclusions
Assay performance can be modeled as dependent on viral load, fit using laboratory bench study results, and adjusted to account for direct-specimen testing. When using nasopharyngeal specimens, direct testing on Abbott ID NOW and VTM testing on DiaSorin Simplexa have similar performance.