bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hyperbolic matrix factorization improves prediction of drug-target associations
Authors: Poleksic Aleksandar 
Published: January 2023

AbstractPast research in computational systems biology has focused more on the development and applications of advanced statistical and numerical optimization techniques and much less on understanding the geometry of the biological space. By representing biological entities as points in a low dimensional Euclidean space, state-of-the-art methods for drug-target interaction (DTI) prediction implicitly assume the flat geometry of the biological space. In contrast, recent theoretical studies suggest that biological systems exhibit tree-like topology with a high degree of clustering. As a consequence, embedding a biological system in a flat space leads to distortion of distances between biological objects. Here, we present a novel matrix factorization methodology for drug-target interaction prediction that uses hyperbolic space as the latent biological space. When benchmarked against classical, Euclidean methods, hyperbolic matrix factorization exhibits superior accuracy while lowering embedding dimension by an order of magnitude. We see this as additional evidence that the hyperbolic geometry underpins large biological networks.
Short photoperiod modulates behavior, cognition and hippocampal neurogenesis in male Japanese quail
Authors: Georgelin Marion , Ferreira Vitor Hugo Bessa , Cornilleau Fabien , Meurisse Maryse , Poissenot Kévin , Beltramo Massimiliano , Keller Matthieu , Lansade Léa , Dardente Hugues , Calandreau Ludovic 
Published: January 2023

AbstractThe mechanisms underlying the photoperiodic control of reproduction in mammals and birds have been recently clarified. In contrast, the potential impact of photoperiod on more complex, integrative processes, such as cognitive behaviors, remains poorly characterized. Here, we investigated the impact of contrasted long and short photoperiods (LP, 16 h light/day and SP, 8 h light/day, respectively) on learning, spatial orientation abilities, and emotional reactivity in male Japanese quail. In addition, we quantified cell proliferation and young cell maturation/migration within the hippocampus, a brain region involved in spatial orientation. Our study reveals that, in male quail, SP increases emotional responses and spatial orientation abilities, compared to LP. Behaviorally, SP birds were found to be more fearful than LP birds, exhibiting more freezing in the open field and taking longer to exit the dark compartment in the emergence test. Furthermore, SP birds were significantly less aggressive than LP birds in a mirror test. Cognitively, SP birds were slower to habituate and learn a spatial orientation task compared to LP birds. However, during a recall test, SP birds performed better than LP birds. From a neuroanatomical standpoint, SP birds had a significantly lower density of young neurons, and also tended to have a lower density of mature neurons within the hippocampus, compared to LP birds. In conclusion, our data reveal that, beyond breeding control, photoperiod also exerts a profound influence on behavior, cognition, and brain plasticity, which comprise the seasonal program of this species.
Switchable synthesis of natural-product-like lawsones and indenopyrazoles through regioselective ring-expansion of indantrione
Authors: Hu Bingwei , Yan Wenxin , Jiang Peiyun , Jiang Ling , Yuan Xu , Lin Jun , Jiao Yinchun , Jin Yi 
Published: January 2023

AbstractLawsones and indenopyrazoles are the prevalent structural motifs and building blocks in pharmaceuticals and bioactive molecules, but their synthesis has always remained challenging as no comprehensive protocol has been outlined to date. Herein, a metal-free, ring-expansion reaction of indantrione with diazomethanes, generated in situ from the N-tosylhydrazones, has been developed for the synthesis of lawsone and indenopyrazole derivatives in acetonitrile and alcohol solvents, respectively. It provides these valuable lawsone and pyrazole skeletons in good yields and high levels of diastereoselectivity from simple and readily available starting materials. DFT calculations were used to explore the mechanism in different solutions. The synthetic application example also showed the prospects of this method for the preparation of valuable compounds.
Pneumologische Rehabilitation bei Long Covid –
Gesundheitliche Veränderungen am Ende der stationären
Rehabilitationsmaßnahme
Authors: Rutsch Mercedes , Frommhold Jördis , Buhr-Schinner Heike , Gross Thomas , Schüller Per Otto , Deck Ruth 
Published: January 2023

Zusammenfassung
Hintergrund Ein Teil der Covid-19-Erkrankten kann über die akute
Krankheitsphase hinaus von persistierenden Symptomen und langfristigen
Krankheitsfolgen (Long Covid) betroffen sein, die wiederum
Teilhabeieinschränkungen zur Folge haben können. Deshalb richtet
sich der Blick verstärkt auf die medizinische Rehabilitation, die mit
Long Covid vor Herausforderungen gestellt wird.
Methodik Es wird eine prospektive, exploratorische Beobachtungsstudie
durchgeführt. Die schriftliche Befragung von
Long-Covid-Rehabilitand*innen findet am Anfang und Ende der
pneumologischen Rehabilitation statt. Ziel der Studie ist die Beschreibung der
Reha-Inhalte und -Ziele, der subjektiven Belastungen, der sozialen und
beruflichen Teilhabe sowie der gesundheitsbezogenen Veränderungen.
Erhoben wurden u. a. krankheitsspezifische Symptome,
Lebensqualität, Teilhabe, psychische Beeinträchtigungen, Fatigue
sowie Leistungsfähigkeit.
Ergebnisse Es nahmen N=221 Long-Covid-Rehabilitand*innen
im Rahmen ihres Heilverfahrens an der schriftlichen Befragung teil. Die
Fragebogenerhebung zeigt am Ende der Rehabilitation bei fast allen
Outcomeparametern signifikante Verbesserungen mit großem Effekt
(p<0.01; ES zwischen 0.76 (Ängstlichkeit) und 1.30 (Fatigue)).
Sämtliche Corona-Symptome, wie Luftnot bei Belastung, Abgeschlagenheit
oder Kraftlosigkeit, verbessern sich signifikant zum Ende der Reha mit ebenfalls
zum Teil großem Effekt. Am häufigsten nennen die
Rehabilitand*innen als Reha-Ziel die Verbesserung ihrer Gesundheit
(92%), Erhöhung ihrer Leistungsfähigkeit (92%)
und Verbesserung der Atemmuskelkraft (78%). Diese Ziele werden von 60
bis 70% erreicht, deutlich weniger Rehabilitand*innen erreichen
die Wiederherstellung der Arbeitsfähigkeit (32%) oder eine
bessere Konzentrationsfähigkeit (17%). Die Atemphysiotherapie,
das Ausdauertraining und die Medizinische Trainingstherapie werden als am
hilfreichsten beschrieben. Am Ende der Rehabilitation bewerten 76% ihren
Reha-Erfolg anhand einer Einzelfrage als gut bis ausgezeichnet.
Schlussfolgerungen Die ersten Daten der Studie zeigen, dass
Long-Covid-Patient*innen erheblichen Belastungen ausgesetzt sind. Durch
die medizinische Rehabilitation erleben die Betroffenen medizinische und soziale
Unterstützung und erreichen signifikante Verbesserungen in allen
erfassten gesundheitsbezogenen Zielgrößen.
Prehospital Cardiac Arrest Should be Considered When Evaluating Coronavirus Disease 2019 Mortality in the United States
Authors: Williams Nick 
Published: January 2023

Abstract
Background Public health emergencies leave little time to develop novel surveillance efforts. Understanding which preexisting clinical datasets are fit for surveillance use is of high value. Coronavirus disease 2019 (COVID-19) offers a natural applied informatics experiment to understand the fitness of clinical datasets for use in disease surveillance.
Objectives This study evaluates the agreement between legacy surveillance time series data and discovers their relative fitness for use in understanding the severity of the COVID-19 emergency. Here fitness for use means the statistical agreement between events across series.
Methods Thirteen weekly clinical event series from before and during the COVID-19 era for the United States were collected and integrated into a (multi) time series event data model. The Centers for Disease Control and Prevention (CDC) COVID-19 attributable mortality, CDC's excess mortality model, national Emergency Medical Services (EMS) calls, and Medicare encounter level claims were the data sources considered in this study. Cases were indexed by week from January 2015 through June of 2021 and fit to Distributed Random Forest models. Models returned the variable importance when predicting the series of interest from the remaining time series.
Results Model r2 statistics ranged from 0.78 to 0.99 for the share of the volumes predicted correctly. Prehospital data were of high value, and cardiac arrest (CA) prior to EMS arrival was on average the best predictor (tied with study week). COVID-19 Medicare claims volumes can predict COVID-19 death certificates (agreement), while viral respiratory Medicare claim volumes cannot predict Medicare COVID-19 claims (disagreement).
Conclusion Prehospital EMS data should be considered when evaluating the severity of COVID-19 because prehospital CA known to EMS was the strongest predictor on average across indices.
Costimulatory Molecules OX40 and OX40L Upregulation in Oral Squamous Cell Carcinoma: A Blood-Based Study
Authors: Sani Aliya Irshad , Rubab Zila , Usman Shumaila , Ahmed Syed Zaryab , Arif Sadia 
Published: January 2023

AbstractObjectives This research aimed to determine OX40 and OX40L mRNA expression in blood samples of naive oral squamous cell carcinoma (OSCC) patients in different histological grades and clinical stages. The in silico analysis was performed using the STRING database for functional association and a better understanding of the interactions of OX40 and its ligand with other proteins.Materials and Methods In this study, we recruited 141 newly diagnosed patients of OSCC. Levels of OX40 and OX40L mRNA expression were explored using real-time quantitative polymerase chain reaction. An in silico tool was also utilized to evaluate the OX40/OX40L interactome.Results The results showed higher OX40 expressional levels in the late stage (23-fold) compared with the early stage (8.5-fold) (p = < 0.001). A similar trend was seen in OX40L mRNA expression, revealing a fold change of 5.8 in the early stage in comparison to 9.9-fold change in the late stage (p = < 0.001). Overexpression of OX40 and OX40L was found in different histological grades (p = 0.005 and p = < 0.001, respectively). Overexpression of OX40 and OX40L was detected in habits such as smoking and paan intake, whereas statistically significant upregulation was observed in the cheek, lip, and alveolus tumors. However, there was no substantial difference in OX40 and OX40L expression based on age or gender. The functional interactions, that is, interactomes of OX40 and OX40L with other proteins have been determined by in silico analysis.Conclusion Based on current study findings, despite OX40 and OX40L upregulation in newly diagnosed OSCC patients, it is speculated that the physiological function of these molecules is altered due to immune system exhaustion.
Histopathological Evaluation of Angiogenic Markers in Non-Hodgkin's Lymphoma
Authors: Singh Priyanka , Tahlan Anita , Mohan Harsh , Singh Ram 
Published: January 2023

Abstract
Background Angiogenesis plays a key role in the development, maintenance, and progression of tumor. The incidence of non-Hodgkin's lymphoma (NHL) is increasing from the past three decades.
Materials and Methods The aim of the study is to evaluate microvessel density (MVD) using CD34 monoclonal antibody and vascular endothelial growth factor (VEGF) using monoclonal antibody that were studied in pretreatment paraffin-embedded tissue samples of 60 cases.
Results MVD was found to be increased in parallel with increasing grade of tumor. B-NHL had a mean MVD of 79.5 ± 8.8 (no./mm2), while T-NHL had a mean MVD of 183 ± 37.6 (no./mm2). VEGF expression was seen in 42 cases (70%), 20 cases (33.3%) showed strong VEGF expression, and the remainder showed either weak (36.6%) or no (30%) staining. Strong VEGF expression is seen in 100% cases of T-NHL and 77.7% cases of B-NHL. Mean MVD and VEGF expression was found to be correlated significantly with the histological grade of NHL (p = 0.001 and p = 0.000, respectively). Average microvessel counts were 53, 82.9, and 130.8 vessels (no./mm2) for negative, weak, and strong VEGF staining, respectively. These differences were statistically significant (p = 0.005 for strong vs. negative and p = 0.091 for strong vs. weak VEGF staining individually).
Conclusion As the grade of tumor progresses, the angiogenic potential also advances which seems to depend on VEGF. The presence of higher MVD in high-grade lymphomas can be utilized for antiangiogenic drugs.
Ritlecitinib (PF-06651600), an oral JAK3/TEC inhibitor, stabilizes active lesions and promotes re-pigmentation of stable lesions in patients with active nonsegmental vitiligo: results from a phase 2b, randomized, placebo-controlled, dose-ranging study
Authors: Yamaguchi Yuji , Peeva Elena , Shore Ronald , Han George , Cox Lori Ann , Banerjee Anindita , Thaci Diamant , Hamzavi Iltefat , Sloan Abigail , Ganesan Anand K , Ezzedine Khaled 
Published: January 2023

Abstract
Patients with active nonsegmental vitiligo (NSV) may experience active lesions (confetti-like and trichrome lesions) or stable lesions (where lesions may remain unchanged for ∼1 year or more). In a phase 2b trial, the oral JAK3/TEC inhibitor ritlecitinib demonstrated a significant improvement in the Facial-Vitiligo Area Scoring Index at Week 24 for patients with active NSV at 50 mg daily with or without a loading dose (100 or 200 mg daily for 4 weeks). To evaluate the efficacy of ritlecitinib on active vs. stable lesions in patients with active NSV who participated in the phase 2b trial (NCT0371529). Patients were randomized to daily ritlecitinib or placebo for 24 weeks, with or without a 4-week loading dose: 200/50, 100/50, 50, 30, 10 mg, or placebo. Mean percent change from baseline (%CFB) in depigmentation extent (100%, 90%, 75%, 50%, 25%, or 10%) within the lesion at baseline and Week 24 was evaluated centrally using photographs obtained from both active (clinical signs including confetti-like and trichrome lesions) and stable target lesions, other than on the face. The analysis included 317 patients who had active and stable lesions simultaneously among 364 treated patients. Within active lesions, ritlecitinib induced a statistically significant reduction in depigmentation extent [%CFB: 200/50 mg, +0·8 (P = 0·0388); 100/50 mg, −1·7 (P = 0·0035); 30 mg, −1·6 (P = 0·0086)] compared with a progressive increase in depigmentation in the placebo group (%CFB: +5·6). No significant reduction was seen with ritlecitinib 50 mg (+2·8) or 10 mg (+1·4%). Within stable lesions, ritlecitinib showed a statistically significant reduction in depigmentation extent, reflecting re-pigmentation [%CFB: 200/50 mg, −7·2 (P = 0·0045); 100/50 mg, −6·1 (P = 0·0082); 50 mg, −5·9 (P = 0·0134); 30 mg, −8·0 (P = 0·0092)] compared with the placebo group, where %CFB in de-pigmentation increased (%CFB: +0·5). No significant reduction was seen with ritlecitinib 10 mg (−3·3%). The magnitude of the re-pigmentation was numerically greater in stable lesions compared with that in active lesions. In patients with active NSV, ritlecitinib treatment for 24 weeks stabilized active lesions and promoted re-pigmentation of stable lesions.
NMR investigation on gas desorption characteristics in CBM recovery during dewatering in deep and shallow coals
Authors: Sun Yingfeng , Lin Qingxia , Zhu Shuaipeng , Han Chujian , Wang Xiaoliang , Zhao Yixin 
Published: January 2023

Abstract
Coalbed methane (CBM) development requires dewatering until the reservoir pressure is less than the critical desorption pressure. Significant quantities of CBM in China are buried &gt;1000 m deep. Therefore, the desorption characteristics of deep CBM reservoirs must be investigated for the further development of deep CBM. In this study, the variation laws of adsorbed and free CH4 during adsorption in dry samples and during desorption via dewatering are investigated using nuclear magnetic resonance. During CH4 adsorption in dry samples by increasing CH4 pressure and during CH4 desorption in water-injected samples by dewatering, a Langmuir relationship exists between the volume of adsorbed CH4 and the pressure in deep and shallow coals, and the volume of free CH4 and the pressure are linearly related. When the pressure is the same, the volume of adsorbed CH4 in the dry coal samples during adsorption is larger than that in the water-injected samples during desorption by dewatering. When the pressure is the same, for the difference in the adsorbed CH4 volume between adsorption and desorption isotherms, shallow coal is less significant than deep coal. The slopes of free CH4 in deep coal are lower than those in shallow coal during adsorption and desorption.
Excavation unloading response of cylindrical rock-like specimen with axial joints: laboratory experiment and numerical simulation
Authors: Hou Gongyu , Zhou Yuliang , Zhao Tielin , Tan Jinxing , Zhao Qinru , Huang Jiamin 
Published: January 2023

Abstract
Joints have a significant influence on the deformation and failure mechanism of the surrounding rock. To reveal the influence of axial joint on mechanical response of the roadway surrounding rock after excavation unloading, the deformation and failure characteristics of cylindrical rock-like specimen (CRLS) with an axial joint was studied through laboratory tests and numerical simulation. Also, the influence of joint size and position on strain variation, secondary stress evolution and plastic zone distribution of the CRLS were analyzed. Results show that the axial joint can promote the deformation of the surrounding rock on the inner side of the joint, while hindering the deformation of the surrounding rock of the roadway on the outer side of the joint. In addition, the size and position of the axial joint have a significant influence on the distribution of secondary stress and plastic zone of the surrounding rock. The stress relief zone is mainly located between the joint and the excavation profile, whereas the plastic zone is mainly distributed at both ends of the joint and between the joint and the excavation profile. Finally, the tangential stress concentration can be alleviated by choosing proper distance between the joints and the roadway, and the failure mode of the surrounding rock between the joint and the excavation profile transmitted from tensile failure to shear failure with the axial joint moves away from the roadway. The research results could provide technical reference for roadway support and disaster prevention in a deep jointed rock mass.
Management of Impella device fracture during direct aortic explantation
Authors: Jackson W Landon , Kepford Matthew J , Yamane Shane S , Carabello John F , Boyer Kryston R 
Published: January 2023

Abstract
The utilisation of mechanical circulatory support devices in patients undergoing high-risk coronary artery bypass continues to increase. The Impella is a ventricular assist device commonly used in the setting of post-cardiotomy cardiogenic shock. This device can be implanted directly into the ascending aorta during open cardiac surgery. Device fracture is a documented complication of the Impella; however, the management of device fracture during direct explantation from an aortic graft has not yet been described. We report a case of Impella device fracture during its removal from a prosthetic aortic graft and discuss the management of this complication.
High Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Prevalence After the Third Epidemic Wave (May–October 2021) in Matadi, Democratic Republic of the Congo
Authors: Munyeku-Bazitama Yannick , Okitale-Talunda Patient , Mpingabo-Ilunga Patrick , Yambayamba Marc K , Tshiminyi Paul M , Umba-Phuati Aimé , Kimfuta Jacques , Phukuta Ferdinand A , Makindu Goethe , Mufwaya-Nsene Raymond , Asari Ryoko , Makimoto Saeda , Baketana Lionel K , Ahuka-Mundeke Steve , Isono Mitsuo , Nsio-Mbeta Justus , Makiala-Mandanda Sheila , Muyembe-Tamfum Jean-Jacques 
Published: January 2023

Abstract

Background
By the end of the third wave of the coronavirus disease 2019 (COVID-19) epidemic (May–October 2021), only 3130 of the 57 268 confirmed cases of coronavirus disease 2019 (COVID-19) in the Democratic Republic of the Congo (DRC) were reported in Kongo Central. This province, and especially its capital city, Matadi, has essential trade and exchanges with Kinshasa, the epicenter of the COVID-19 epidemic in DRC. Kinshasa accounted for 60.0% of all cases during the same period. The true burden of COVID-19 in Matadi is likely underestimated. In this study, we aimed to determine the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence and associated risk factors after the third wave in Matadi.

Methods
We conducted a population-based cross-sectional study in October 2021. Consenting participants were interviewed and tested using an enzyme-linked immunosorbent assay commercial kit. We applied univariable and multivariable analysis to evaluate factors associated with seropositivity and adjusted the seroprevalence for the test kit performance.

Results
We included 2210 participants from 489 households. Female participants represented 59.1%. The median age was 27 years (interquartile range, 16–45 years). The crude SARS-CoV-2 seroprevalence was 82.3%. Age was identified as the main risk factor as younger age decreased the seropositivity odds. Accounting for clustering at the household level increased the seroprevalence to 83.2%. The seroprevalence increased further to 88.1% (95% confidence interval, 86.2%–90.1%) after correcting for the laboratory test kit performance.

Conclusions
The SARS-CoV-2 seroprevalence was very high, contrasting with reported cases. Evidence generated from this population-based survey remains relevant in guiding the local COVID-19 response, especially vaccination strategies.
Comparing Complication Rates of Midline Catheter vs Peripherally Inserted Central Catheter. A Systematic Review and Meta-analysis
Authors: Urtecho Meritxell , Torres Roldan Victor D , Nayfeh Tarek , Espinoza Suarez Nataly R , Ranganath Nischal , Sampathkumar Priya , Chopra Vineet , Safdar Nasia , Prokop Larry J , O’Horo John C 
Published: January 2023

Abstract

Background
Peripherally inserted central catheters (PICCs) and midlines are commonly used devices for reliable vascular access. Infection and thrombosis are the main adverse effects of these catheters. We aimed to evaluate the relative risk of complications from midlines and PICCs.

Methods
We conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) and observational studies. The primary outcomes were catheter-related bloodstream infection (CRBSI) and thrombosis. Secondary outcomes evaluated included mortality, failure to complete therapy, catheter occlusion, phlebitis, and catheter fracture. The certainty of evidence was assessed using the GRADE approach.

Results
Of 8368 citations identified, 20 studies met the eligibility criteria, including 1 RCT and 19 observational studies. Midline use was associated with fewer patients with CRBSI compared with PICCs (odds ratio [OR], 0.24; 95% CI, 0.15–0.38). This association was not observed when we evaluated risk per catheter. No significant association was found between catheters when evaluating risk of localized thrombosis and pulmonary embolism. A subgroup analysis based on location of thrombosis showed higher rates of superficial venous thrombosis in patients using midlines (OR, 2.30; 95% CI, 1.48–3.57). We did not identify any significant difference between midlines and PICCs for the secondary outcomes.

Conclusions
Our findings suggest that patients who use midlines might experience fewer CRBSIs than those who use PICCs. However, the use of midline catheters was associated with greater risk of superficial vein thrombosis. These findings can help guide future cost-benefit analyses and direct comparative RCTs to further characterize the efficacy and risks of PICCs vs midline catheters.