bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Can Progress Toward Ending the Human Immunodeficiency Virus Epidemic in the United States Be Monitored?
Authors: Mitchell Kate M , Maheu-Giroux Mathieu , Dimitrov Dobromir , Moore Mia , Hughes James P , Donnell Deborah , Beyrer Chris , El-Sadr Wafaa M , Cohen Myron S , Boily Marie Claude 
Published: November 2021

Abstract
The plan for Ending the HIV (human immunodeficiency virus) Epidemic (EHE) in the United States aims to reduce new infections by 75% by 2025 and by 90% by 2030. For EHE to be successful, it is important to accurately measure changes in numbers of new HIV infections after 5 and 10 years (to determine whether the EHE goals have been achieved) but also over shorter timescales (to monitor progress and intensify prevention efforts if required). In this viewpoint, we aim to demonstrate why the method used to monitor progress toward the EHE goals must be carefully considered. We briefly describe and discuss different methods to estimate numbers of new HIV infections based on longitudinal cohort studies, cross-sectional incidence surveys, and routine surveillance data. We particularly focus on identifying conditions under which unadjusted and adjusted estimates based on routine surveillance data can be used to estimate changes in new HIV infections.
Five-year outcomes in trials comparing transcatheter aortic valve implantation versus surgical aortic valve replacement: a pooled meta-analysis of reconstructed time-to-event data
Authors: Barili Fabio , Freemantle Nicholas , Musumeci Francesco , Martin Barbara , Anselmi Amedeo , Rinaldi Mauro , Kaul Sanjay , Rodriguez-Roda Jorge , Di Mauro Michele , Folliguet Thierry , Verhoye Jean-Philippe , Sousa-Uva Miguel , Parolari Alessandro ,   the Latin European Alliance of CardioVascular Surgical Societies (LEACSS) and with the endorsement of the Latin American Association of Cardiac and Endovascular Surgery (LACES), LEACSS members are the Italian Society of Cardiac Surgery (FB FM MR MdM AP), the Portuguese Society of Cardiac Surgery (MSU), the French Society of Cardiac Surgery (JFV, AA) and the Spanish Society of Cardiac Surgery (JRR) Institutions
Published: November 2021

Abstract

OBJECTIVES
The incidence of outcomes in trials comparing transcatheter aortic valve implantation (TAVI) and surgical aortic valve replacement (SAVR) is expected to be different in the short and long term. We planned a meta-analysis of reconstructed time-to-event data from trials comparing TAVI and SAVR to evaluate their time-varying effects on outcomes.

METHODS
We performed a systematic review of the literature from January 2007 through September 2021 on Medline, Embase, the Cochrane Central Register of Controlled Trials and specialistic websites, including randomized trials with allocation to TAVI or SAVR that reported at least 1-year follow-up and that graphed Kaplan–Meier curves of end points. The comparisons were done with grouped frailty Cox models in a landmark framework and fully parametric models.

RESULTS
Seven trials were included (7770 participants). TAVI showed a lower incidence of the composite of death or stroke in the first 6 months [risk-stratified hazard ratio (HR) 0.66, 95% confidence interval (CI) 0.56–0.77, P-value &lt;0.001], with an HR reversal after 24 months favouring SAVR (risk-stratified HR 1.25; 95% CI 1.08–1.46; P-value 0.003). These outcomes were confirmed for all-cause death (risk-stratified HR after 24 months 1.18; 95% CI 1.03–1.35; P-value 0.01). TAVI was also associated with an increased incidence of rehospitalization after 6 months (risk-stratified HR 1.42; 95% CI 1.06–1.91; P-value 0.018) that got worse after 24 months (risk-stratified HR 1.67; 95% CI 1.24–2.24; P-value &lt;0.001).

CONCLUSIONS
Although it could appear that there is no difference between TAVI and SAVR in the 5-year cumulative results, TAVI shows a strong protective effect in the short term that runs out after 1 year. TAVI becomes a risk factor for all-cause mortality and the composite end point after 24 months and for rehospitalization after 6 months.
What makes Komagataella phaffii non-conventional?
Authors: Ata Özge , Ergün Burcu Gündüz , Fickers Patrick , Heistinger Lina , Mattanovich Diethard , Rebnegger Corinna , Gasser Brigitte 
Published: November 2021

ABSTRACT
The important industrial protein production host Komagataella phaffii (syn Pichia pastoris) is classified as a non-conventional yeast. But what exactly makes K. phaffii non-conventional? In this review, we set out to address the main differences to the ‘conventional’ yeast Saccharomyces cerevisiae, but also pinpoint differences to other non-conventional yeasts used in biotechnology. Apart from its methylotrophic lifestyle, K. phaffii is a Crabtree-negative yeast species. But even within the methylotrophs, K. phaffii possesses distinct regulatory features such as glycerol-repression of the methanol-utilization pathway or the lack of nitrate assimilation. Rewiring of the transcriptional networks regulating carbon (and nitrogen) source utilization clearly contributes to our understanding of genetic events occurring during evolution of yeast species. The mechanisms of mating-type switching and the triggers of morphogenic phenotypes represent further examples for how K. phaffii is distinguished from the model yeast S. cerevisiae. With respect to heterologous protein production, K. phaffii features high secretory capacity but secretes only low amounts of endogenous proteins. Different to S. cerevisiae, the Golgi apparatus of K. phaffii is stacked like in mammals. While it is tempting to speculate that Golgi architecture is correlated to the high secretion levels or the different N-glycan structures observed in K. phaffii, there is recent evidence against this. We conclude that K. phaffii is a yeast with unique features that has a lot of potential to explore both fundamental research questions and industrial applications.
Regularizing linear inverse problems under unknown non-Gaussian white noise allowing repeated measurements
Authors: Harrach Bastian , Jahn Tim , Potthast Roland 
Published: November 2021

Abstract
We deal with the solution of a generic linear inverse problem in the Hilbert space setting. The exact right-hand side is unknown and only accessible through discretized measurements corrupted by white noise with unknown arbitrary distribution. The measuring process can be repeated, which allows to reduce and estimate the measurement error through averaging. We show convergence against the true solution of the infinite-dimensional problem for a priori and a posteriori regularization schemes as the number of measurements and the dimension of the discretization tend to infinity under natural and easily verifiable conditions for the discretization.
SAT: a Surrogate-Assisted Two-wave case boosting sampling method, with application to EHR-based association studies
Authors: Liu Xiaokang , Chubak Jessica , Hubbard Rebecca A , Chen Yong 
Published: November 2021

Abstract

Objectives
Electronic health records (EHRs) enable investigation of the association between phenotypes and risk factors. However, studies solely relying on potentially error-prone EHR-derived phenotypes (ie, surrogates) are subject to bias. Analyses of low prevalence phenotypes may also suffer from poor efficiency. Existing methods typically focus on one of these issues but seldom address both. This study aims to simultaneously address both issues by developing new sampling methods to select an optimal subsample to collect gold standard phenotypes for improving the accuracy of association estimation.

Materials and Methods
We develop a surrogate-assisted two-wave (SAT) sampling method, where a surrogate-guided sampling (SGS) procedure and a modified optimal subsampling procedure motivated from A-optimality criterion (OSMAC) are employed sequentially, to select a subsample for outcome validation through manual chart review subject to budget constraints. A model is then fitted based on the subsample with the true phenotypes. Simulation studies and an application to an EHR dataset of breast cancer survivors are conducted to demonstrate the effectiveness of SAT.

Results
We found that the subsample selected with the proposed method contains informative observations that effectively reduce the mean squared error of the resultant estimator of the association.

Conclusions
The proposed approach can handle the problem brought by the rarity of cases and misclassification of the surrogate in phenotype-absent EHR-based association studies. With a well-behaved surrogate, SAT successfully boosts the case prevalence in the subsample and improves the efficiency of estimation.
Validated Spectrophotometric Methods for Simultaneous Determination of Atorvastatin Calcium and Olmesartan Medoxomil in Their Pharmaceutical Formulation
Authors: Kamal Amira H , Hammad Sherin F , Marie Aya A 
Published: November 2021

Abstract

Background
Few spectrophotometric methods have been developed for the simultaneous determination of atorvastatin calcium (ATO) and olmesartan medoxomil (OLM).

Objective
This work aimed to develop and validate five simple spectrophotometric methods for the simultaneous estimation of ATO and OLM in their tablet form.

Methods
Method I applied the area under curve (AUC) based on the measurement of areas between 241 and 261 nm for ATO, and 248 and 263 nm for OLM. Method II applied second derivative spectrophotometry where the analytical amplitudes at 246.5 and 235 nm were chosen for the estimation of ATO and OLM, respectively. Method III applied the ratio difference (RD) method based on the measurement of amplitude difference (ΔP) within ratio spectra; ΔP (240–260 nm) was directly related to ATO concentration, and ΔP (262–240 nm) was directly related to OLM concentration. Method IV depended on the absorbance ratio method in which the wavelength at the iso-absorptive point (λISP) and the maximum absorbance wavelength (λmax), 277 and 255.5 nm, respectively, were used to calculate OLM concentration, while ATO concentration was determined from the zero-order UV spectra at 300 nm. Method V utilized a dual wavelength (DW) technique where ΔA between 247.5 and 262 nm was directly related to ATO concentration, and ΔA between 216 and 238 nm was directly related to OLM concentration.

Results
The results of the assays indicated good mean % recovery ± SD as well as good agreement with the reported method.

Conclusion
Five simple and rapid spectrophotometric methods were developed, validated, and successfully applied for simultaneous estimation of ATO and OLM tablets.

Highlights
None of the developed methods has previously been reported for simultaneous determination of ATO and OLM.
HPLC–MS Analysis of Four Potential Genotoxic Impurities in Alogliptin Pharmaceutical Materials
Authors: Al-Sabti Bashar , Harbali Jehad 
Published: November 2021

Abstract

Background
Pyridine, 3-aminopyridine, 4-dimethylaminopyridine, and N, N-dimethylamine are reactive bases that may be used in the preparation of the pharmaceutical ingredient alogliptin (ALO). They are considered as potentially genotoxic impurities (PGIs) since they contain electrophilic functional groups. Therefore, they should be monitored at the allowed limits in ALO.

Objective
The aim of this study was to develop a novel liquid chromatography–mass spectrometry (LC–MS) method to estimate quantities of pyridine, 3-aminopyridine, 4-dimethylaminopyridine, and N, N-dimethylaniline impurities in ALO drug material.

Methods
The separation was performed on Kromasil CN (250 mm × 3.9 mm, 3.5 µm) column in reversed phase mode. The mobile phase was a mixture of water-methanol (55:45, v/v) containing 2.5 mM ammonium acetate and 0.1% formic acid. Impurities were detected by MS in selected ion monitoring mode at m/z = 80, 95, 122, and 123 for pyridine, 3-aminopyridine, N, N-dimethylaniline, and 4-dimethylaminopyridine, respectively. The flow rate of the method was 0.5 mL/min.

Results
The sensitivity of the method was excellent at levels much less than the allowed limits. The method had excellent linearity in the concentration ranges of Quantitation Limit (QL)-150% of allowed limits and coefficients of determination were above 0.9990. The recovery ratios were in the range of 93.56–110.28%.

Conclusion
Results showed good linearity, precision, accuracy, sensitivity, selectivity, robustness, and solution stability. The studied method was applied to test two samples of raw materials and one sample of tablets.

Highlights
The method discussed here could be very useful for controlling potentially genotoxic impurities (PGIs) levels in ALO during its synthesis, and for QC testing of ALO raw materials before using them in the preparation of pharmaceutical products.
Experiments on Multiple Requests for Consent to Data Linkage in Surveys
Authors: Walzenbach Sandra , Burton Jonathan , Couper Mick P , Crossley Thomas F , JÄckle Annette 
Published: November 2021

Abstract
It is increasingly common for researchers to link survey data to administrative data. If several administrative data sources are of interest, respondents are required to give consent to each of them, meaning that multiple consent questions have to be included in one survey. Existing literature suggests that individual consent varies widely between data sources and over time, but little is known about how respondents process multiple consent requests in a single survey. Using an online access panel in Great Britain, we conducted a set of experiments in two surveys to explore multiple consent requests (covering five domains or data sources). In the first study, we experimentally varied the format of the request, testing three versions: (1) a sequence of pages (with one response per domain), (2) all five requests on the same page (with one response per domain), and (3) a single request (with one joint request covering all five domains). We also varied the order of the domains. We find that average consent rates do not differ by format, but asking a less-sensitive or easier-to-comply request first yields slightly higher average consent rates than asking a more sensitive request first. We repeated the order experiment in a second study, using an independent sample from the same panel, and adding two more order conditions. We find average consent rates are not affected much by order, but the consent to individual domains is affected by order. However, we fail to replicate the pattern of consents found in the first study. We conclude that the order in which multiple consent requests are asked does matter, but in complicated ways that depend on the particular outcomes in which one is interested. Objective knowledge and subjective comprehension of the consent process, and confidence in the decision are largely unaffected by format or order.
The return of the spin period in DW Cnc and evidence of new high state outbursts
Authors: Duffy C , Ramsay G , Steeghs D , Kennedy M R , West R G , Wheatley P J , Dhillon V S , Ackley K , Dyer M J , Galloway D K , Gill S , Acton J S , Burleigh M R , Casewell S L , Goad M R , Henderson B A , Tilbrook R H , Strøm P A , Anderson D R 
Published: November 2021

ABSTRACT
DW Cnc is an intermediate polar which has previously been observed in both high and low states. Observations of the high state of DW Cnc have previously revealed a spin period at ∼38.6 min, however, observations from the 2018 to 2019 low state showed no evidence of the spin period. We present results from our analysis of 12 s cadence photometric data collected by Next Generation Transit Survey of DW Cnc during the high state which began in 2019. Following the previously reported suppression of the spin period signal, we identify the return of this signal during the high state, consistent with previous observations of it. We identify this as the restarting of accretion during the high state. We further identified three short outbursts lasting ∼1 d in DW Cnc with a mean recurrence time of ∼60 d and an amplitude of ∼1 mag. These are the first outbursts identified in DW Cnc since 2008. Due to the short nature of these events, we identify them not as a result of accretion instabilities but instead either from instabilities originating from the interaction of the magnetorotational instability in the accretion disc and the magnetic field generated by the white dwarf or the result of magnetic gating.
CoBiToM Project – II. Evolution of contact binary systems close to the orbital period cut-off
Authors: Loukaidou G A , Gazeas K D , Palafouta S , Athanasopoulos D , Zola S , Liakos A , Niarchos P G , Hakala P , Essam A , Hatzidimitriou D 
Published: November 2021

ABSTRACTUltra-short orbital period contact binaries (Porb &lt; 0.26 d) host some of the smallest and least massive stars. These systems are faint and rare, and it is believed that they have reached a contact configuration after several Gyrs of evolution via angular momentum loss, mass transfer, and mass loss through stellar wind processes. This study is conducted in the frame of the Contact Binaries Towards Merging (CoBiToM) Project and presents the results from light curve and orbital analysis of 30 ultra-short orbital period contact binaries, with the aim to investigate the possibility of them being red nova progenitors, eventually producing merger events. Approximately half of the systems exhibit orbital period modulations, as a result of mass transfer or mass loss processes. Although they are in contact, their fill-out factor is low (less than 30 per cent), while their mass ratio is larger than the one in longer period contact binaries. This study investigates the orbital stability of these systems and examines their physical and orbital parameters in comparison to those of the entire sample of known and well-studied contact binaries, based on combined spectroscopic and photometric analysis. It is found that ultra-short orbital period contact binaries have very stable orbits, while very often additional components are gravitationally bound in wide orbits around the central binary system. We confirmed that the evolution of such systems is very slow, which explains why the components of ultra-short orbital period systems are still Main Sequence stars after several Gyrs of evolution.
Aberrant Cerebello-Thalamo-Cortical Functional and Effective Connectivity in First-Episode Schizophrenia With Auditory Verbal Hallucinations
Authors: Wei Yarui , Xue Kangkang , Yang Meng , Wang Huan , Chen Jingli , Han Shaoqiang , Wang Xiaoxiao , Li Hong , Zhang Yong , Song Xueqin , Cheng Jingliang 
Published: November 2021

Abstract
The thalamus is known to be impaired in schizophrenia patients with auditory verbal hallucinations (AVHs). Abnormal filtering function of the thalamus has been found in schizophrenia patients with AVHs. However, a whole-structure approach has commonly been adopted when investigating thalamic dysconnectivity in patients with AVHs, and it remains unclear which thalamic nucleus is the critical structure underlying AVHs. Here, we investigated voxel-wise resting-state functional connectivity (rsFC) of the thalamic nucleus in drug-naïve patients with first-episode schizophrenia (FES) with AVHs. In addition, dynamic causal modeling was applied to compute effective connectivity and estimate causal relationships that could explain aberrant rsFC. Compared with the FES patients without AVH (NAVH) and normal controls, patients with AVHs had weaker rsFC of the bilateral medial pulvinar (PuM) nucleus-cerebellum. Moreover, compared with the normal control group, the AVH and NAVH groups had significantly stronger rsFC of the bilateral PuM nucleus-cerebral cortex, as well as weaker rsFC of the right medial geniculate nucleus-cerebral cortex. Compared with the NAVH and normal control groups, dynamic causal modeling revealed significantly stronger effective connectivity from the left PuM nucleus to the right inferior frontal gyrus in the AVH group. These findings indicate that the critical structure in the thalamus underlying AVHs is the PuM nucleus, and provide direct evidence that the cerebello-thalamo-cortical circuit is associated with AVHs.
Phylodynamic analysis and spike protein mutations in porcine deltacoronavirus with a new variant introduction in Taiwan
Authors: Hsueh Fu-Chun , Wu Cheng-Nan , Lin Marco Yung-Cheng , Hsu Feng-Yang , Lin Chuen-Fu , Chang Hui-Wen , Lin Jih-Hui , Liu Hsin-Fu , Chiou Ming-Tang , Chan Kuan Rong , Lin Chao-Nan 
Published: November 2021

Abstract
Porcine deltacoronavirus (PDCoV) is a highly transmissible intestinal pathogen that causes mild to severe clinical symptoms, such as anorexia, vomiting, and watery diarrhea in pigs. By comparing the genetic sequences of the spike glycoprotein between historical and current Taiwanese PDCoV strains, we identified a novel PDCoV variant that displaced the PDCoV responsible for the 2015 epidemic. This PDCoV variant belongs to a young population within the US lineage, and infected pigs carry high concentrations of the virus. It also has several critical point mutations and an amino acid insertion at position 52 that may enhance the affinity between the B-cell epitopes located in the N-terminal domain with its complementarity regions, consequently facilitating binding or penetration between the fusion peptide and cellular membrane. Furthermore, viral protein structure prediction demonstrated that these amino acid changes may change the ability of the virus to bind to the receptor, which may consequently alter virus infectivity. Our results hence suggest the emergence of new PDCoV strains in Taiwan with the potential for greater transmission and pathogenesis.
Reevaluating race and the glomerular filtration rate calculator
Authors: Lyas Claretha , Zuber Kim , Davis Jane 
Published: November 2021

ABSTRACT
Estimated glomerular filtration rate (eGFR) calculators have included a race adjustment to help approximate measured GFR. Over the past several years, as more attention has been directed toward uncovering racial bias, the appropriateness of including race in these calculators has been called into question. The American Society of Nephrology and the National Kidney Foundation convened an expert task force to review the inclusion of race in eGFR. The deliberative review showed that race can be removed from eGFR calculators without causing adverse reactions in any group of patients. This new, refitted CKD-EPI equation can be used immediately by all laboratories in the United States. The task force also recommended greater use of cystatin C nationally in eGFR calculations. This would enable the new CKD-EPI equation to incorporate both creatinine and cystatin C without race and would yield better accuracy than a calculator that uses creatinine alone.
Delivery Technique for Fibular Strut Bone Grafting to Proximal Humerus Nonunion Fractures
Authors: Kane Steven M. , Tanaka Scott , Smith Matt 
Published: November 2021

Introduction:
The prevalence of proximal humerus fractures will continue to increase as the population ages. Although the use of fibular strut grafts to treat these fractures is well established and has been used for many years, the authors present an alternative technique that aligns the graft within the intermedullary canal, and proximal segment, allowing for greater fragment and reduction control throughout the procedure.

Materials and Methods:
The technique involves intramedullary reaming and the usage of a #5 suture through the strut graft proximally that allows for easy placement of the graft across the fracture and into the humeral head after reduction.

Results:
The representative case described in this paper demonstrates a simplified technique for placement of a fibular allograft and fracture reduction with locking plate fixation for the treatment of proximal humerus nonunions.

Discussion:
The technique is an effective and simple method for the placement of a fibular strut allograft within the intramedullary canal of the distal and proximal segments of a proximal humeral fracture. The use of an endosteal fibular allograft strut addresses the need to re-establish the medial column of the humerus, provides local bone stock, and helps avoid varus angulation, and allows for improved fixation of the plate in poor quality bone.