bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Multiple Waves of COVID-19 in Patients With Inflammatory Bowel Disease: A Temporal Trend Analysis
Authors: Kaplan Gilaad G , Underwood Fox E , Coward Stephanie , Agrawal Manasi , Ungaro Ryan C , Brenner Erica J , Gearry Richard B, , Kissous-Hunt Michele , Lewis James D , Ng Siew C , Rahier Jean-Francois , Reinisch Walter , Steinwurz Flavio , Zhang Xian , Kappelman Michael D , Colombel Jean-Frederic 
Published: January 2022

Abstract

Background
Cases of coronavirus disease 2019 (COVID-19) have emerged in discrete waves. We explored temporal trends in the reporting of COVID-19 in inflammatory bowel disease (IBD) patients.

Methods
The Surveillance Epidemiology of Coronavirus Under Research Exclusion for Inflammatory Bowel Disease (SECURE-IBD) is an international registry of IBD patients diagnosed with COVID-19. The average percent changes (APCs) were calculated in weekly reported cases of COVID-19 during the periods of March 22 to September 12, September 13 to December 12, 2020, and December 13 to July 31, 2021.

Results
Across 73 countries, 6404 cases of COVID-19 were reported in IBD patients. COVID-19 reporting decreased globally by 4.2% per week (95% CI, −5.3% to −3.0%) from March 22 to September 12, 2020, then climbed by 10.2% per week (95% CI, 8.1%-12.3%) from September 13 to December 12, 2020, and then declined by 6.3% per week (95% CI, −7.8% to −4.7%). In the fall of 2020, weekly reporting climbed in North America (APC, 11.3%; 95% CI, 8.8-13.8) and Europe (APC, 17.7%; 95% CI, 12.1%-23.5%), whereas reporting was stable in Asia (APC, −8.1%; 95% CI, −15.6-0.1). From December 13, 2020, to July 31, 2021, reporting of COVID-19 in those with IBD declined in North America (APC, −8.5%; 95% CI, −10.2 to −6.7) and Europe (APC, −5.4%; 95% CI, −7.2 to −3.6) and was stable in Latin America (APC, −1.5%; 95% CI, −3.5% to 0.6%).

Conclusions
Temporal trends in reporting of COVID-19 in those with IBD are consistent with the epidemiological patterns COVID-19 globally.
Tofacitinib Inhibits Leukocyte Trafficking Across the Intestinal Endothelial Barrier in a Specific Cohort of Ulcerative Colitis Patients
Authors: Massimino Luca , Spanò Salvatore , Lamparelli Luigi Antonio , Fuggetta Davide , Peyrin-Biroulet Laurent , Sileri Pierpaolo , Danese Silvio , D’Alessio Silvia , Ungaro Federica 
Published: January 2022

Lay Summary
The JAK/STAT inhibitor tofacitinib, recently approved for the treatment of ulcerative colitis, is found to modulate the intestinal endothelial barrier functions in directing the leukocyte adhesion and transmigration in ulcerative colitis patients displaying high levels of endothelial STAT3/STAT6 phosphorylation.
Zouglou Visions of Transitional Justice
Authors: Kouadio Lyn J -V 
Published: January 2022

ABSTRACT∞
This article argues that through Zouglou music, Ivorian youths have defined what it means to deliver justice in the wake of violence by positioning Zouglou and Zouglou-Nouchi “ways of being” as an inescapable means of political legitimation. Beginning with the turn from Houphouët’s single party rule to multiparty politics in 1990, to the 2002–2007 and 2010–2011 eras of violent conflict, Zouglou artists, themselves youths, have shaped the terms of democratic transition. They have crafted a space wherein to discuss the meanings of violent conflict and justice as well as opened possibilities for youths to shape what the Ivorian democratic future should be. In doing so, youths have prescribed new ways of political legitimation. As a result, in Côte d’Ivoire politicians do not only vie for the presidential seat but also engage with Zouglou and Zouglou-Nouchi “ways of being” to gain popular affection.
Nonparametric regression on low-dimensional manifolds using deep ReLU networks: function approximation and statistical recovery
Authors: Chen Minshuo , Jiang Haoming , Liao Wenjing , Zhao Tuo 
Published: January 2022

AbstractReal-world data often exhibit low-dimensional geometric structures and can be viewed as samples near a low-dimensional manifold. This paper studies nonparametric regression of Hölder functions on low-dimensional manifolds using deep Rectified Linear Unit (ReLU) networks. Suppose $n$ training data are sampled from a Hölder function in $\mathcal{H}^{\ s,\alpha }$ supported on a $d$-dimensional Riemannian manifold isometrically embedded in $\mathbb{R}^D$. A deep ReLU network architecture is designed to estimate the underlying function from the training data. The mean squared error of the empirical estimator is proved to converge in the order of $n^{-\frac{2(s+\alpha )}{2(s+\alpha ) + d}}\log ^3 n$. This result shows that deep ReLU networks give rise to a fast convergence rate depending on the data intrinsic dimension $d$, which is usually much smaller than the ambient dimension $D$. It therefore demonstrates the adaptivity of deep ReLU networks to low-dimensional geometric structures in data and partially explains the power of deep ReLU networks in tackling high-dimensional data with low-dimensional geometric structures.
Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires
Authors: Campos Gabriel Soares , Cardoso Fernando Flores , Gomes Claudia Cristina Gulias , Domingues Robert , de Almeida Regitano Luciana Correia , de Sena Oliveira Marcia Cristina , de Oliveira Henrique Nunes , Carvalheiro Roberto , Albuquerque Lucia Galvão , Miller Stephen , Misztal Ignacy , Lourenco Daniela 
Published: January 2022

Abstract
Genomic prediction has become the new standard for genetic improvement programs, and currently, there is a desire to implement this technology for the evaluation of Angus cattle in Brazil. Thus, the main objective of this study was to assess the feasibility of evaluating young Brazilian Angus (BA) bulls and heifers for 12 routinely recorded traits using single-step genomic BLUP (ssGBLUP) with and without genotypes from American Angus (AA) sires. The second objective was to obtain estimates of effective population size (Ne) and linkage disequilibrium (LD) in the Brazilian Angus population. The dataset contained phenotypic information for up to 277,661 animals belonging to the Promebo breeding program, pedigree for 362,900, of which 1,386 were genotyped for 50k, 77k, and 150k single nucleotide polymorphism (SNP) panels. After imputation and quality control, 61,666 SNPs were available for the analyses. In addition, genotypes from 332 American Angus (AA) sires widely used in Brazil were retrieved from the AA Association database to be used for genomic predictions. Bivariate animal models were used to estimate variance components, traditional EBV, and genomic EBV (GEBV). Validation was carried out with the linear regression method (LR) using young-genotyped animals born between 2013 and 2015 without phenotypes in the reduced dataset and with records in the complete dataset. Validation animals were further split into progeny of BA and AA sires to evaluate if their progenies would benefit by including genotypes from AA sires. The Ne was 254 based on pedigree and 197 based on LD, and the average LD (±SD) and distance between adjacent single nucleotide polymorphisms (SNPs) across all chromosomes were 0.27 (±0.27) and 40743.68 bp, respectively. Prediction accuracies with ssGBLUP outperformed BLUP for all traits, improving accuracies by, on average, 16% for BA young bulls and heifers. The GEBV prediction accuracies ranged from 0.37 (total maternal for weaning weight and tick count) to 0.54 (yearling precocity) across all traits, and dispersion (LR coefficients) fluctuated between 0.92 and 1.06. Inclusion of genotyped sires from the AA improved GEBV accuracies by 2%, on average, compared to using only the BA reference population. Our study indicated that genomic information could help us to improve GEBV accuracies and hence genetic progress in the Brazilian Angus population. The inclusion of genotypes from American Angus sires heavily used in Brazil just marginally increased the GEBV accuracies for selection candidates.
Soil Invertebrates Generate Microplastics From Polystyrene Foam Debris
Authors: Helmberger Maxwell S , Miesel Jessica R , Tiemann Lisa K , Grieshop Matthew J 
Published: January 2022

Abstract
To fully understand microplastics' impact on soil ecosystems, one must recognize soil organisms as not just passively enduring their negative effects, but potentially contributing to microplastics' formation, distribution, and dynamics in soil. We investigated the ability of four soil invertebrates, the cricket Gryllodes sigillatus Walker (Orthoptera: Gryllidae), the isopod Oniscus asellus L. (Isopoda: Oniscidae), larvae of the beetle Zophobas morio Fabricius (Coleoptera: Tenebrionidae), and the snail Cornu aspersum Müller (Stylommatophora: Helicidae) to fragment macroscopic pieces of weathered or pristine polystyrene (PS) foam. We placed invertebrates into arenas with single PS foam pieces for 24 h, then collected and assessed the microplastic content of each invertebrate's fecal material, its cadaver, and the sand substrate of its arena via hydrogen peroxide digestion, filtration, and fluorescent staining. All taxa excreted PS particles, though snails only to a tiny extent. Beetle larvae produced significantly more microplastics than snails, and crickets and isopods fragmented the weathered PS foam pieces more than the pristine pieces, which they left untouched. A follow-up experiment with pristine PS foam assessed the effect of different treatments mimicking exposure to the elements on fragmentation by isopods. PS foam pieces soaked in a soil suspension were significantly more fragmented than untreated pieces or pieces exposed to UV light alone. These findings indicate that soil invertebrates may represent a source of microplastics to the environment in places polluted with PS foam trash, and that the condition of macroplastic debris likely affects its palatability to these organisms.
Case of resected small-cell neuroendocrine carcinoma of the extrahepatic bile duct
Authors: Sugita Hiroaki , Maeda Kazuya , Nishikawa Satoshi , Doden Kenji , Hashizume Yasuo 
Published: January 2022

Abstract
Neuroendocrine carcinomas (NECs) arising from the extrahepatic bile duct (EHBD) are extremely rare, and their preoperative diagnosis is difficult. A small number of resected cases of EHBD NECs has been reported, and their prognosis is usually poor. A 62-year-old man presented with obstructive jaundice and liver disease. Radiological imaging revealed wall thickness and stricture of the distal common bile duct (CBD); however, lymph node or distant metastasis was not detected. Adenocarcinoma was detected on biopsy, and surgery was performed with a preoperative diagnosis of cholangiocarcinoma of the distal CBD. Pathological examination revealed adenocarcinoma of the CBD mucosa (20%) and NEC of the CBD wall (80%). The final pathological diagnosis was small-cell NEC of the EHBD. His post-operative course was good, and there was no recurrence for 4 months after surgery. Herein, we report a case of resected EHBD NEC and a literature review.
Urinary MMP-7: A Predictive, Noninvasive Early Marker for Chronic Kidney Disease Development in Patients with Hypertension
Authors: Sarangi RajLaxmi , Tripathy Krishna Padarabinda , Bahinipati Jyotirmayee , Gupta Partisha , Pathak Mona , Mahapatra Srikrushna , Mohapatra Soumya R 
Published: January 2022

AbstractObjectiveUpregulation of matrix metalloproteinase-7 (MMP-7) is associated with hypertension and kidney fibrosis, which can progress to chronic kidney disease (CKD). Currently, kidney fibrosis is only detectable by an invasive procedure. Therefore, we set out to determine whether MMP-7 can act as a noninvasive biomarker in patients with hypertension to enable early detection of kidney fibrosis.Materials and MethodsDiagnosed patients with hypertension and control patients were sampled. We diagnosed CKD using clinical and laboratory parameters. Serum urea, creatinine, urinary microalbumin, the albumin-to-creatinine ratio, and urinary MMP-7 were analyzed.ResultsThe 195 patients with hypertension had significantly elevated MMP-7. Of these patients, 166 had MMP-7 &gt;25.8 μg/L, whereas only 29 had MMP-7 &lt;25.8 μg/L. Thirty-two patients with hypertension showed features of CKD, all of whom had urinary MMP-7 &gt;25.8 μg/L. However, the urinary MMP-7 level did not differ with the severity of CKD or with the duration of hypertension.ConclusionElevated urinary MMP-7 can be a potential noninvasive, early indicator in patients with hypertension progressing to CKD, thus enabling early therapeutic intervention.
Forward modelling the O3(a+b) GW transient mass distributions with bpass by varying compact remnant mass and SNe kick prescriptions
Authors: Ghodla Sohan , van Zeist Wouter G J , Eldridge J J , Stevance Héloïse F , Stanway Elizabeth R 
Published: January 2022

ABSTRACT
We present forward modelling from the bpass code suite of the population of observed gravitational wave (GW) transients reported by the LIGO/VIRGO consortium (LVC) during their third observing run, O3(a+b). Specifically, we predict the expected chirp mass and mass ratio distributions for GW transients, taking account of detector sensitivity to determine how many events should have been detected by the current detector network in O3(a+b). We investigate how these predictions change by alternating between four different remnant mass estimation schemes and two supernovae (SNe) kick prescriptions. We find that none of the model populations resulting from these variations accurately match the whole O3(a+b) GW transient catalogue. However, agreement from some models to part of the catalogue suggests ways to achieve a more complete fit. These include reducing the number of low-mass black holes (BHs) close to the mass gap, while also increasing the number of higher mass BHs below the pair-instability SN limit. Finally, we find that the interaction between the value of the remnant mass from a stellar model and the choice of SN kick is complex and different kick prescriptions may be required depending on whether a neutron star or BH is formed.
Eukaryotic stress–induced mutagenesis is limited by a local control of translesion synthesis
Authors: Masłowska Katarzyna H , Villafañez Florencia , Laureti Luisa , Iwai Shigenori , Pagès Vincent 
Published: January 2022

Abstract
The DNA damage response (DDR) preserves the genetic integrity of the cell by sensing and repairing damages after a genotoxic stress. Translesion Synthesis (TLS), an error-prone DNA damage tolerance pathway, is controlled by PCNA ubiquitination. In this work, we raise the question whether TLS is controlled locally or globally. Using a recently developed method that allows to follow the bypass of a single lesion inserted into the yeast genome, we show that (i) TLS is controlled locally at each individual lesion by PCNA ubiquitination, (ii) a single lesion is enough to induce PCNA ubiquitination and (iii) PCNA ubiquitination is imperative for TLS to occur. More importantly, we show that the activation of the DDR that follows a genotoxic stress does not increase TLS at individual lesions. We conclude that unlike the SOS response in bacteria, the eukaryotic DDR does not promote TLS and mutagenesis.
CT-FOCS: a novel method for inferring cell type-specific enhancer–promoter maps
Authors: Hait Tom Aharon , Elkon Ran , Shamir Ron 
Published: January 2022

AbstractSpatiotemporal gene expression patterns are governed to a large extent by the activity of enhancer elements, which engage in physical contacts with their target genes. Identification of enhancer–promoter (EP) links that are functional only in a specific subset of cell types is a key challenge in understanding gene regulation. We introduce CT-FOCS (cell type FOCS), a statistical inference method that uses linear mixed effect models to infer EP links that show marked activity only in a single or a small subset of cell types out of a large panel of probed cell types. Analyzing 808 samples from FANTOM5, covering 472 cell lines, primary cells and tissues, CT-FOCS inferred such EP links more accurately than recent state-of-the-art methods. Furthermore, we show that strictly cell type-specific EP links are very uncommon in the human genome.
Sublithosphere Mantle Crystallization and Immiscible Sulfide Melt Segregation in Continental Basalt Magmatism: Evidence from Clinopyroxene Megacrysts in the Cenozoic Basalts of Eastern China
Authors: Sun Pu , Niu Yaoling , Guo Pengyuan , Duan Meng , Wang Xiaohong , Gong Hongmei 
Published: January 2022

AbstractThis study explores the effects of high-pressure crystallization and immiscible sulfide melt segregation under mantle conditions on the compositional variation of basaltic magmas, using clinopyroxene megacrysts in the Cenozoic basalts of eastern China. These clinopyroxene megacrysts are large (up to &gt;10 cm in size) and homogeneous at the grain scale. They were crystallized from variably evolved parental magmas and then captured by their host basalts. The large and systematic variations of [Sm/Yb]N, Lu/Hf, Fe/Mn, Sc/La, Ni and Cu with Mg# in the clinopyroxene megacrysts suggest their co-precipitation with garnet and with immiscibility between sulfide and silicate melts. This is consistent with the appearance of garnet megacrysts in the host basalts and abundant sulfide globules in the clinopyroxene megacrysts. The covariation between Ni contents of sulfide globules and Mg# of the clinopyroxene megacrysts suggests a genetic relationship between sulfide globules and clinopyroxene megacrysts. High-pressure crystallization of clinopyroxene and garnet results in decrease of Mg# and concentrations of CaO, MnO and heavy rare earth elements (e.g. Yb) and increase of Fe/Mn and [Sm/Yb]N in the residual melts. Therefore, geochemical characteristics of low Mg#, low CaO and MnO contents and high Fe/Mn and [Sm/Yb]N in basalts do not necessarily indicate a pyroxenite mantle source. In addition, caution is needed when applying the olivine addition method to infer the primary compositions of alkali basalts without considering the effects of high-pressure crystallization of clinopyroxene and garnet. The calculated pressure (P) and temperature (T) conditions of the clinopyroxene megacrysts are close to those of the lithosphere–asthenosphere boundary (LAB) beneath eastern China, and the low primitive [Sm/Yb]N (~4.0) of melts parental to the clinopyroxene megacrysts suggests final equilibration at relatively low pressures most likely beneath the LAB. Hence, a melt-rich layer is expected close beneath the LAB. Melt pools in this melt-rich layer provide a stable and closed environment for the growth of compositionally homogeneous clinopyroxene megacrysts. As a result, melts in these melt pools are compositionally evolved with low and variable Mg#. Subsequent pulses of melt aggregation/supply from depths with primitive compositions and high Mg# will disturb these melt pools, cause magma mixing and trigger the eruption of magmas carrying clinopyroxene and garnet megacrysts.
The R2R3-MYB transcription factor FaMYB63 participates in regulation of eugenol production in strawberry
Authors: Wang Shuaishuai , Shi Mengyun , Zhang Yang , Pan Zhifei , Xie Xingbin , Zhang Linzhong , Sun Peipei , Feng Huan , Xue Hao , Fang Congbing , Zhao Jing 
Published: January 2022

Abstract
The biosynthetic pathway of volatile phenylpropanoids, including 4-allyl-2-methoxyphenol (eugenol), has been investigated in petunia (Petunia hybrida). However, the regulatory network for eugenol accumulation in strawberry (Fragaria × ananassa Duch.) fruit remains unclear. Here, an R2R3-type MYB transcription factor (TF; FaMYB63) was isolated from strawberry by yeast one-hybrid (Y1H) screening using the promoter of the FaEGS1 (eugenol synthase 1 [EGS 1]) gene, which encodes the enzyme responsible for the last step in eugenol biosynthesis. FaMYB63 is phylogenetically distinct from other R2R3-MYB TFs, including FaEOBІІ (EMISSION OF BENZENOID II [EOBII]), which also participates in regulating eugenol biosynthesis in strawberry receptacles. Reverse transcription quantitative PCR (RT-qPCR) assays showed that the expression of FaMYB63 was tissue-specific and consistent with eugenol content through strawberry fruit development, was repressed by abscisic acid, and was activated by auxins (indole-3-acetic acid). Overexpression and RNA interference-mediated silencing of FaMYB63 resulted in marked changes in the transcript levels of the biosynthetic genes FaEGS1, FaEGS2, and FaCAD1 (cinnamyl alcohol dehydrogenase 1 [CAD1]) and, thereby, the accumulation of eugenol. Electrophoretic mobility shift, Y1H, GUS activity, and dual-luciferase activity assays demonstrated that the transcript levels of FaEOBІІ and FaMYB10 were regulated by FaMYB63, but not the other way around. Together, these results demonstrate that FaMYB63 directly activates FaEGS1, FaEGS2, FaCAD1, FaEOBІІ, and FaMYB10 to induce eugenol biosynthesis during strawberry fruit development. These findings deepen the understanding of the regulatory network that influences eugenol metabolism in an edible fruit crop.
The Long-Term Analgesic Effectiveness of Platelet-Rich Plasma Injection for Carpal Tunnel Syndrome: A Cross-Sectional Cohort Study
Authors: Lai Chia-Ying , Li Tsung-Ying , Lam King Hei Stanley , Chou Yu-Ching , Hueng Dueng-Yuan , Chen Liang-Cheng , Wu Yung-Tsan 
Published: January 2022

Abstract

Objective
Interest in perineural platelet-rich-plasma (PRP) injections for the treatment of carpal tunnel syndrome (CTS) has increased in recent years. However, evidence supporting the long-term effectiveness of PRP is lacking. Therefore, the aim of our cross-sectional cohort study was to investigate the long-term results of PRP injections for CTS.

Methods
Eighty-one patients diagnosed with CTS of any grade who received a single PRP injection at least 2 years prior were enrolled. Through structured telephone interviews, all patients were asked of their post-injection outcomes compared to their pre-injection condition. Symptom relief ≥50%, compared to the pre-injection condition, was considered an effective outcome. Binary logistic regression was applied to analyze each baseline variable as a regressor for determining the prognostic outcome factors.

Results
In total, 70% of patients reported positive outcomes ≥2 years post-injection. Shorter duration of symptoms before treatment (odds ratio: 0.991; 95% confidence interval [CI] 0.983–0.999; P = .023) and lower electrodiagnostic severity of CTS were the main prognostic factors for an effective outcome (mild grade vs severe grade, odds ratio: 17.652; 95% CI 1.43–221.1; P = .025). Although there was a trend toward positive outcomes at longer follow-up durations (2–3 years vs 3–4 years vs 4–5 years), the difference was not statistically significant.

Conclusions
A single perineural PRP injection has a long-term analgesic effect on CTS, especially in mild-to-moderate cases.
The stability and dynamics of computationally designed proteins
Authors: Gonzalez Natali A , Li Brigitte A , McCully Michelle E 
Published: January 2022

AbstractProtein stability, dynamics and function are intricately linked. Accordingly, protein designers leverage dynamics in their designs and gain insight to their successes and failures by analyzing their proteins’ dynamics. Molecular dynamics (MD) simulations are a powerful computational tool for quantifying both local and global protein dynamics. This review highlights studies where MD simulations were applied to characterize the stability and dynamics of designed proteins and where dynamics were incorporated into computational protein design. First, we discuss the structural basis underlying the extreme stability and thermostability frequently observed in computationally designed proteins. Next, we discuss examples of designed proteins, where dynamics were not explicitly accounted for in the design process, whose coordinated motions or active site dynamics, as observed by MD simulation, enhanced or detracted from their function. Many protein functions depend on sizeable or subtle conformational changes, so we finally discuss the computational design of proteins to perform a specific function that requires consideration of motion by multi-state design.