bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biphasic regulation of transcriptional surge generated by the gene feedback loop in a two-component system
Authors: Liu Wen , Li Xiang , Qi Hong , Wu Yuning , Qu Jing , Yin Zhiyong , Gao Xuejuan , Han Aidong , Shuai Jianwei 
Published: February 2021

Abstract

Motivation
Transcriptional surges generated by two-component systems (TCSs) have been observed experimentally in various bacteria. Suppression of the transcriptional surge may reduce the activity, virulence and drug resistance of bacteria. In order to investigate the general mechanisms, we use a PhoP/PhoQ TCS as a model system to derive a comprehensive mathematical modeling that governs the surge. PhoP is a response regulator, which serves as a transcription factor under a phosphorylation-dependent modulation by PhoQ, a histidine kinase.

Results
Our model reveals two major signaling pathways to modulate the phosphorylated PhoP (P-PhoP) level, one of which promotes the generation of P-PhoP, while the other depresses the level of P-PhoP. The competition between the P-PhoP-promoting and the P-PhoP-depressing pathways determines the generation of the P-PhoP surge. Furthermore, besides PhoQ, PhoP is also a bifunctional modulator that contributes to the dynamic control of P-PhoP state, leading to a biphasic regulation of the surge by the gene feedback loop. In summary, the mechanisms derived from the PhoP/PhoQ system for the transcriptional surges provide a better understanding on such a sophisticated signal transduction system and aid to develop new antimicrobial strategies targeting TCSs.

Availability and implementation
https://github.com/jianweishuai/TCS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Inference on the average treatment effect under minimization and other covariate-adaptive randomization methods
Authors: Ye Ting , Yi Yanyao , Shao Jun 
Published: February 2021

SummaryCovariate-adaptive randomization schemes such as minimization and stratified permuted blocks are often applied in clinical trials to balance treatment assignments across prognostic factors. The existing theory for inference after covariate-adaptive randomization is mostly limited to situations where a correct model between the response and covariates can be specified or the randomization method has well-understood properties. Based on stratification with covariate levels utilized in randomization and a further adjustment for covariates not used in randomization, we propose several model-free estimators of the average treatment effect. We establish the asymptotic normality of the proposed estimators under all popular covariate-adaptive randomization schemes, including the minimization method, and we show that the asymptotic distributions are invariant with respect to covariate-adaptive randomization methods. Consistent variance estimators are constructed for asymptotic inference. Asymptotic relative efficiencies and finite-sample properties of estimators are also studied. We recommend using one of our proposed estimators for valid and model-free inference after covariate-adaptive randomization.
Pattern of recurrence in patients with a pathologically complete response after neoadjuvant chemoradiotherapy and surgery for oesophageal cancer
Authors: de Jongh M , Eyck B M , van der Werf L R , Toxopeus E L A , van Lanschot J J B , Lagarde S M , van der Gaast A , Nuyttens J , Wijnhoven B P L 
Published: February 2021

Abstract

Background
Neoadjuvant chemoradiotherapy (nCRT) and surgery is a widely used treatment for locally advanced resectable oesophageal cancer, with 20–50 per cent of patients having a pathological complete response (pCR). Disease, however, still recurs in 20–30 per cent of these patients. The aim of this study was to assess the pattern of recurrence in patients with a pCR after nCRT and surgery.

Methods
All patients with a pCR after nCRT and surgery included in the phase II and III CROSS (ChemoRadiotherapy for Oesophageal followed by Surgery Study) trials (April 2001 to December 2008) and after the CROSS trials (September 2009 to October 2017) were identified. The site of recurrence was compared with the applied radiation and surgical fields. Outcomes were median time to recurrence, and overall and progression-free survival.

Results
A total of 141 patients with a median follow-up of 100 (i.q.r. 64–134) months were included. Some 29 of 141 patients (20,6 per cent) developed recurrence. Of these, four had isolated locoregional recurrence, 15 had distant recurrence only, and ten had both locoregional and distant recurrence. Among the 14 patients with locoregional recurrences, five had recurrence within the radiation field, seven outside the radiation field, and two at the border. Median time to recurrence was 24 (10–62) months. The 5-year overall survival rate was 74 per cent and the recurrence-free survival rate was 70 per cent.

Conclusion
Despite good overall survival, recurrence still occurred in 21 per cent of patients. Most recurrences were distant, outside the radiation and surgical fields.
Postoperative outcome after reoperative isolated tricuspid valve surgery—is there a predictor for survival?
Authors: Pfannmueller Bettina , Budde Luca-Marie , Etz Christian D , Noack Thilo , Cuartas Mateo Marin , Misfeld Martin , Borger Michael A 
Published: February 2021

Abstract

OBJECTIVES
Reoperative tricuspid valve (TV) surgery is considered high risk even in the absence of additional concomitant cardiac procedures. The purpose of this study was to evaluate preoperative clinical parameters as predictors for survival after isolated reoperative TV surgery.

METHODS
From January 2005 to January 2019, 85 patients (mean age: 66.7 ± 10.3 years, 34 male) with severe isolated TV regurgitation and prior cardiac surgery were referred to our centre for elective or urgent TV repair/replacement; patients with endocarditis were excluded. We retrospectively analysed preoperative hepatorenal function [reflected by widely used clinical and laboratory parameters and the Model of End-stage-Liver Disease excluding International Normalized Ratio (MELD-XI) score] as a predictor for postoperative survival.

RESULTS
At hospital admission, the patients’ average preoperative New York Heart Association class was 2.9 ± 0.6, left ventricular ejection fraction 52.5 ± 10.6%, mean pulmonary artery pressure 24.7 ± 8.0 mmHg, creatinine 115.4 ± 66.6 μmol/l, bilirubin 20.0 ± 19.6 μmol/l and the mean MELD-XI score was 13.3 ± 4.0 μmol/l. The mean follow-up was 5.4 ± 4.2 years. Thirty-day mortality was 5%, 5-year survival was 60.6 ± 5.4% and 10-year survival was 42.9 ± 6.5%. The multivariable Cox regression analysis evaluated the MELD-XI score [hazard ratio (HR 1.144, confidence interval 95% 1.0–1.3, P = 0.005] and diabetes mellitus (HR 2.27, confidence interval 95% 1.0–5.0, P = 0.04) as significant predictors for excess mortality while age and mean pulmonary artery pressure did not reliably predict clinical outcome.

CONCLUSIONS
Hepatorenal dysfunction was one main factor accounting for limited postoperative survival in our patient cohort. The MELD-XI score is easy to calculate and seems to reliably predict the perioperative risk in patients with prior cardiac surgery and indication for TV surgery.
Vertical stability of different orthognathic treatments for correcting skeletal anterior open bite: a systematic review and meta-analysis
Authors: Wang Mengqiao , Zhang Bowen , Li Lan , Zhai Mingrui , Wang Zhengyan , Wei Fulan 
Published: February 2021

Summary

Background
Several orthognathic procedures have been applied to correct skeletal anterior open bites (SAOB). Which method is most stable has been debated and no consensus has been reached and there is no conclusive evidence for clinicians to use.

Objective
To analyse whether maxillary, mandibular, or bimaxillary surgery provides a better stability.

Materials and methods
A systematic search was conducted up to December 2020 using PubMed, EMBASE, Medline, Scopus, Web of Science, Cochrane CENTRAL, and Google Scholar. We made direct comparisons among the controlled trials and also made indirect comparisons via subgroup analysis on the aspects of occlusional, skeletal, and dento-alveolar stability to assess the overall stability of each method.

Results
Finally 16 cohort studies were identified. At the occlusional level, pooled change in overbite was 0.21 mm in maxillary surgery, 0.37 mm in bimaxillary surgery, and −0.32 mm in mandibular surgery. At the skeletal level, pooled sella–nasion–Point A angle (SNA) was −0.12 degrees in bimaxillary surgery, −0.37 degrees in maxillary surgery and −0.20 degrees in mandibular surgery. The sella–nasion to palatal plane angle (SNPP) relapsed to a statistically significant degree in all samples received single maxillary surgery. Relapse of the sella–nasion–Point B angle (SNB) was 0.47 degrees in mandibular setback, −1.8 degrees in mandibular advancement, and −0.48 degrees in maxillary surgery. The Sella–Nasion to mandibular plane angle (SNMP) relapsed more in procedures involving bilateral sagittal split osteotomy than in other procedures. As for dento-alveolar changes, intrusion of molars and extrusion of incisors took place in most patients.

Conclusions
Bimaxillary surgery produced the most beneficial post-operative increase in overbite, maxillary surgery led to a lesser but still positive overbite change, and mandibular surgery correlated with some extent of relapse. Skeletally, bimaxillary surgery was more stable than maxillary surgery at both SNA and SNPP; SNB was more stable in mandibular setback than advancement; and SNMP was unstable in both mandibular and bimaxillary surgeries versus maxillary surgery with comparable surgical changes. Dento-alveolar compensation helped maintain a positive overbite.

Registration number
CRD42020198088.
Sleep arousal burden is associated with long-term all-cause and cardiovascular mortality in 8001 community-dwelling older men and women
Authors: Shahrbabaki Sobhan Salari , Linz Dominik , Hartmann Simon , Redline Susan , Baumert Mathias 
Published: February 2021

Abstract

Aims
To quantify the arousal burden (AB) across large cohort studies and determine its association with long-term cardiovascular (CV) and overall mortality in men and women.

Methods and results
We measured the AB on overnight polysomnograms of 2782 men in the Osteoporotic Fractures in Men Study (MrOS) Sleep study, 424 women in the Study of Osteoporotic Fractures (SOF) and 2221 men and 2574 women in the Sleep Heart Health Study (SHHS). During 11.2 ± 2.1 years of follow-up in MrOS, 665 men died, including 236 CV deaths. During 6.4 ± 1.6 years of follow-up in SOF, 105 women died, including 47 CV deaths. During 10.7 ± 3.1 years of follow-up in SHHS, 987 participants died, including 344 CV deaths. In women, multivariable Cox proportional hazard analysis adjusted for common confounders demonstrated that AB is associated with all-cause mortality [SOF: hazard ratio (HR) 1.58 (1.01–2.42), P = 0.038; SHHS-women: HR 1.21 (1.06–1.42), P = 0.012] and CV mortality [SOF: HR 2.17 (1.04–4.50), P = 0.037; SHHS-women: HR 1.60 (1.12–2.28), P = 0.009]. In men, the association between AB and all-cause mortality [MrOS: HR 1.11 (0.94–1.32), P = 0.261; SHHS-men: HR 1.31 (1.06–1.62), P = 0.011] and CV mortality [MrOS: HR 1.35 (1.02–1.79), P = 0.034; SHHS-men: HR 1.24 (0.86–1.79), P = 0.271] was less clear.

Conclusions
Nocturnal AB is associated with long-term CV and all-cause mortality in women and to a lesser extent in men.
Core–mantle topographic coupling: a parametric approach and implications for the formulation of a triaxial three-layered Earth rotation
Authors: Zhang Huifeng , Shen Wenbin 
Published: February 2021

SUMMARYWe propose a parametric approach to the topographic (TOP) coupling between the mantle and outer core for refinement of the latest triaxial three-layered Earth rotation theory. Based on three models of the core–mantle boundary (CMB) topography, we obtain the axial components of the TOP torque as −2.08 × 1019, −2.72 × 1018 and −1.97 × 1017 N m, respectively. Under the frame of the triaxial three-layered Earth rotation theory, we solve the corresponding periods of free core nutation as −(329.83 ± 28.12), −(457.54 ± ∼) and −(428.23 ± 1.09) mean solar days (d), respectively. The other three normal modes, namely, Chandler wobble, inner core wobble and free inner core nutation, are almost not affected by the TOP coupling of the CMB, their period values being 433.24, 2718.69 and 934.02 d, respectively. Calculations show that the TOP torque is highly sensitive to the adopted model of the topography, which is known to be robust. Taking into account the normal modes of the triaxial three-layered Earth rotation, the results of the CMB topography obtained by seismic tomography can be constrained in the future to a certain extent. In this study, considering the TOP coupling with the appropriate topography model, the estimates for the dynamic ellipticity ef of the fluid core lie between 0.0026340 and 0.0026430, values that are 3.56 % higher than the hydrostatic equilibrium value.
Endometrial Receptivity Analysis (ERA): data versus opinions
Authors: Ruiz-Alonso Maria , Valbuena Diana , Gomez Carlos , Cuzzi Juliana , Simon Carlos 
Published: February 2021

Abstract
This article summarises and contextualises the accumulated basic and clinical data on the ERA test and addresses specific comments and opinions presented by the opponent as part of an invited debate. Progress in medicine depends on new technologies and concepts that translate to practice to solve long-standing problems. In a key example, combining RNA sequencing data (transcriptomics) with artificial intelligence (AI) led to a clinical revolution in personalising disease diagnosis and fostered the concept of precision medicine. The reproductive field is no exception. Translation of endometrial transcriptomics to the clinic yielded an objective definition of the limited time period during which the maternal endometrium is receptive to an embryo, known as the window of implantation (WOI). The WOI is induced by the presence of exogenous and/or endogenous progesterone (P) after proper oestradiol (E2) priming. The window lasts 30–36 hours and, depending on the patient, occurs between LH + 6 and LH + 9 in natural cycles or between P + 4 and P + 7 in hormonal replacement therapy (HRT) cycles. In approximately 30% of IVF cycles in which embryo transfer is performed blindly, the WOI is displaced and embryo-endometrial synchrony is not achieved. Extending this application of endometrial transcriptomics, the endometrial receptivity analysis (ERA) test couples next-generation sequencing (NGS) to a computational predictor to identify transcriptomic signatures for each endometrial stage: proliferative (PRO), pre-receptive (PRE), receptive (R) and post-receptive (POST). In this way, personalised embryo transfer (pET) may be possible by synchronising embryo transfer with each patient’s WOI. Data are the only way to confront arguments sustained in opinions and/or misleading concepts; it is up to the reader to make their own conclusions regarding its clinical utility.
Plain convergence of adaptive algorithms without exploiting reliability and efficiency
Authors: Gantner Gregor , Praetorius Dirk 
Published: February 2021

Abstract
We consider $h$-adaptive algorithms in the context of the finite element method and the boundary element method. Under quite general assumptions on the building blocks SOLVE, ESTIMATE, MARK and REFINE of such algorithms we prove plain convergence in the sense that the adaptive algorithm drives the underlying a posteriori error estimator to zero. Unlike available results in the literature, our analysis avoids the use of any reliability and efficiency estimate but relies only on structural properties of the estimator, namely stability on nonrefined elements and reduction on refined elements. In particular, the new framework thus also covers problems involving nonlocal operators like the fractional Laplacian or boundary integral equations, where (discrete) efficiency is (currently) not available.
A Review of the Challenges and Complexities in the Diagnosis, Etiology, Epidemiology, and Pathogenesis of Pelvic Inflammatory Disease
Authors: Hillier Sharon L , Bernstein Kyle T , Aral Sevgi 
Published: February 2021

AbstractPelvic inflammatory disease (PID) is a syndrome that causes substantial morbidity, including chronic pelvic pain, to women globally. While limited data are available from low- and middle-income countries, national databases from the United States and Europe suggest that PID incidence may be decreasing but the rate of decrease may differ by the etiologic cause. Recent studies of women with PID have reported that fewer than half of women receiving a diagnosis of PID have gonococcal or chlamydial infection, while Mycoplasma genitalium, respiratory pathogens, and the constellation of bacteria associated with bacterial vaginosis may account for a substantial fraction of PID cases. The clinical diagnosis of PID is nonspecific, creating an urgent need to develop noninvasive tests to diagnose PID. Advances in serologic testing for Chlamydia trachomatis and Neisseria gonorrhoeae could advance epidemiologic studies, while the development of vaccines against these sexually transmitted pathogens could affect incident PID and associated morbidity.
The Association Between Antibody Response to Severe Acute Respiratory Syndrome Coronavirus 2 Infection and Post–COVID-19 Syndrome in Healthcare Workers
Authors: Pereira Christopher , Harris Benjamin H L , Di Giovannantonio Matteo , Rosadas Carolina , Short Charlotte-Eve , Quinlan Rachael , Sureda-Vives Macià , Fernandez Natalia , Day-Weber Isaac , Khan Maryam , Marchesin Federica , Katsanovskaja Ksenia , Parker Eleanor , Taylor Graham P , Tedder Richard S , McClure Myra O , Dani Melanie , Fertleman Michael 
Published: February 2021

AbstractIt is currently unknown how post-COVID-19 syndrome (PCS) may affect those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This longitudinal study includes healthcare staff who tested positive for SARS-CoV-2 between March and April 2020, with follow-up of their antibody titers and symptoms. More than half (21 of 38) had PCS after 7–8 months. There was no statistically significant difference between initial reverse-transcription polymerase chain reaction titers or serial antibody levels between those who did and those who did not develop PCS. This study highlights the relative commonality of PCS in healthcare workers and this should be considered in vaccination scheduling and workforce planning to allow adequate frontline staffing numbers.
Demographics matter: the potentially disproportionate effect of COVID-19 on hospital ratings
Authors: Belasen Ariel R , Tracey Marlon R , Belasen Alan T 
Published: February 2021

AbstractObjectiveTo identify how features of the community in which a hospital serves differentially relate to its patients' experiences based on the quality of that hospital.DesignA Finite Mixture Model (FMM) is used to uncover a mix of two latent groups of hospitals that differ in quality. In the FMM, a multinomial logistic equation relates hospital-level factors to the odds of being in either group. A multiple linear regression relates the characteristics of communities served by hospitals to the patients' expected ratings of their experiences at hospitals in each group. Thus, this association potentially varies with hospital quality. The analysis was conducted via Stata.SettingHospital ratings are measured by Hospital Compare using the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey, a patient satisfaction survey required by the Centers for Medicare and Medicaid Services for hospitals in the USA.Participants2,816 Medicare-certified acute care hospitals across all US states.InterventionNone.Main Outcome MeasureDifferences in the marginal impacts of key community demographics on patient experiences between the two groups of hospitals.ResultsWe provide evidence that low-rated hospitals have much more variability in patient experience ratings than high-rated ones. Moreover, the experiences at low-rated hospitals are more sensitive to county demographic factors, which means exogenous shocks, like coronavirus disease-2019 (COVID-19), will likely affect these hospitals differently, as such shocks are known to disproportionately affect their communities.ConclusionsOur results imply that low-rated hospitals with more variability in their HCAHPS responses are more likely to face adverse patient experiences due to COVID-19 than high-rated hospitals. Pandemics like COVID-19 create conditions that intensify the already high demands placed on hospitals and care providers and make it even more challenging to deliver quality care.
Fecal Microbiota Transplantation for the Treatment of Ulcerative Colitis: A Qualitative Assessment of Patient Perceptions and Experiences
Authors: Chauhan Usha , Popov Jelena , Farbod Yasamin , Kalantar Mona , Wolfe Melanie , Moayyedi Paul , Marshall John K , Halder Smita , Kaasalainen Sharon 
Published: February 2021

Abstract

Background
Fecal microbiota transplantation (FMT) is a promising experimental therapy for ulcerative colitis (UC), yet patient acceptance remains poorly understood.

Aims
The aim of this study was to explore perceptions and experiences of adult patients who received FMT for UC.

Methods
This study used a qualitative descriptive design with thematic content analysis. Patients who were approached for enrollment in a clinical trial (NCT02606032) were invited to participate in face-to-face semistructured interviews. Two groups were interviewed: those who chose to pursue FMT and those who declined FMT. Non-FMT patients were interviewed once; FMT patients were interviewed twice at pre- and post-treatment.

Results
Nine FMT patients (78% female, average age 46.7 years old) and eight non-FMT patients (50% female, average age 39.5 years old) were enrolled. Pretreatment themes included FMT as a natural therapy, external barriers to pursuing FMT, concerns with FMT and factors influencing the decision to pursue FMT. While both groups generally perceived FMT as a natural therapy, pre-FMT patients showed greater acceptance of alternative medicine. Both groups demonstrated poor understanding and similar initial concerns with product cleanliness. Pre-FMT patients were motivated to pursue FMT by feelings of last resort. Post-FMT themes included therapeutic impact of FMT and psychosocial impact of FMT. Post-FMT patients reported overall satisfaction and a unanimous preference for FMT over conventional medications.

Conclusion
This is the first study to assess adult patient perceptions and real-life experiences with FMT for the treatment of UC. By improving patient education, we may achieve greater acceptance of FMT.
Analysis of misaligned journal bearing lubrication performance considering the effect of lubricant couple stress and shear thinning
Authors: Zhu Junchao , Qian Haiyu , Wen Huabing , Zheng Liangyan , Zhu Hanhua 
Published: February 2021

ABSTRACT
This paper investigates journal bearings, and builds a lubrication model taking into account misalignment, the lubricant couple stress effect and shear thinning. In order to explore the sensitivity of couple stress fluid lubrication performance to oil film thickness, we introduce the critical oil film thickness coefficient. The results show that the sensitivity increases with the increase of the couple stress coefficient, and it is highest in the area of minimum oil film thickness. Compared with a parallel journal, increases in the misalignment angle strengthen the effect of couple stress. Shear thinning also plays an important role in bearing lubrication performance. For a low oil inlet temperature, the effect of shear thinning increases with the increase of the couple stress parameter. For a high oil inlet temperature, the influence is negligible. An increase in the misalignment angle will not further enhance the effect of shear thinning.