bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network meta-analysis: efficacy of treatment for acute, chronic, and prevention of pouchitis in ulcerative colitis
Authors: Poo Stephanie , Sriranganathan Danujan , Segal Jonathan P 
Published: March 2022

Introduction
Pouchitis is a clinically significant complication of ileal pouch-anal anastomosis. There is a paucity of head-to-head comparisons between treatments and no data were available about how each treatment rank against each other. A network meta-analysis of the different treatments used for acute, chronic and prevention of pouchitis was conducted.

Methods
Biomedical databases and the Cochrane Central registry were searched between 1978 and 2021 for randomised controlled trials examining treatment for acute, chronic and prevention of pouchitis. A network meta-analysis was performed using the frequentist model with pooled relative risks and P scores used to rank treatments.

Results
18 studies were included from a screen of 4291 abstracts. When compared to placebo, rifaximin was found to be the best antibiotic for acute pouchitis whereas ciprofloxacin ranked highest against metronidazole. For chronic pouchitis, metronidazole followed by probiotics was statistically significant and effective treatments in inducing remission although metronidazole had the highest adverse events. Adalimumab and bismuth were also found to be superior to placebo; however, they did not reach statistical significance. Probiotics proved superior to placebo in the prevention of pouchitis development.

Conclusions
This is the first network meta-analysis which compares the efficacy and tolerability of treatments in the management and prevention of acute and chronic pouchitis. It confirms that antimicrobial therapy remains the mainstay of treatment and adds weight to current guideline recommendations. Our results demonstrate that rifaximin and probiotics may deserve a more prominent role. While biologics are starting to show promise, large-scale head-to-head comparisons are warranted to validate the efficacy of these treatments.
New therapeutics for primary hyperoxaluria type 1
Authors: Dejban Pegah , Lieske John C. 
Published: March 2022

Purpose of review
Primary hyperoxaluria type 1 (PH1) is a rare genetic disorder that causes hepatic overproduction of oxalate and, often, nephrocalcinosis, nephrolithiasis, chronic kidney disease, and kidney failure. The purpose of the review is to provide an update on current emerging therapies for the treatment of PH1.

Recent findings
Use of ribonucleic acid interference (RNAi) therapeutics that target the liver to block production of key enzymes along pathways that generate oxalate is a promising approach. Available evidence supports the efficacy of both Lumasiran (targeting glycolate oxidase) and Nedosiran (targeting hepatic lactate dehydrogenase (LDHa)) to reduce urinary oxalate excretion in PH1. The efficacy of alternative approaches including stiripentol (an anticonvulsant drug that also targets LDHa), lanthanum (a potential gastrointestinal oxalate binder), and Oxalobacter formigenes (a bacterium that can degrade oxalate within the gastrointestinal tract and may also increase its secretion from blood) are all also under study. Genetic editing tools including clustered regularly interspaced short palindromic repeats/Cas9 are also in preclinical study as a potential PH1 therapeutic.

Summary
Novel treatments can reduce the plasma oxalate concentration and urinary oxalate excretion in PH1 patients. Thus, it is possible these approaches will reduce the need for combined kidney and liver transplantation to significantly decrease the morbidity and mortality of affected patients.
Non calcium phosphate binders - Is there any evidence of benefit
Authors: Jadav Paresh R. , Husain S. Ali , Mohan Sumit , Crew Russell 
Published: March 2022

Purpose of review
Low-level evidence and opinion-based clinical practice guidelines highlight the substantial uncertainty in the practice patterns of hyperphosphatemia management in patients with chronic kidney disease (CKD). This manuscript reviews the evidence for the choice of phosphate binders and its impact on clinical outcomes.

Recent findings
Phosphate binders are among the most common medications prescribed for patients on dialysis. Clinical practice guidelines recommend lowering phosphate levels toward normal range and restricting calcium-based binders in all CKD patients. There is substantial gap in the evidence underlying these recommendations with lack of any placebo-controlled, randomized trials showing survival benefits for any class of phosphate-binders. Despite the lack of evidence for specific phosphate target or if lowering phosphate improves survival, use of phosphate binders has remained central strategy in approach to hyperphosphatemia. Use of binders has added to the cost and contributed significant pill burden. Restriction of calcium-based binders to avoid positive calcium balance and consequent vascular calcification risk has a physiological rationale and weight of observational studies.

Summary
There is currently no conclusive evidence that definitively guides the choice of any specific binders for management of hyperphosphatemia in patients with CKD. Use of noncalcium-based binders has a theoretical advantage in restricting total calcium intake to decrease the risk of vascular calcification but no proven benefits for mortality.
Holmium: yttrium-aluminum-garnet laser with Moses: does it make a difference?
Authors: Corsini Christian , de Angelis Mario , Villa Luca , Somani Bhaskar K. , Pietropaolo Amelia , Montorsi Francesco , Goumas Ioannis Kartalas , Traxer Olivier , Salonia Andrea , Ventimiglia Eugenio 
Published: March 2022

Purpose of review
Moses effect is an inherent physical principle of Ho:YAG laser functioning. Moses Technology is a pulse modulation modality of Ho:YAG laser, which became commercially available for the treatment of two urological conditions: urinary stones and benign prostatic obstruction. The purpose of this narrative review is to distinguish between Moses effect and Moses Technology, as well as to summarize the latest evidence on Moses Technology and its main application in the urological field.

Recent findings
During laboratory lithotripsy, Moses Technology seems to reduce stone retropulsion and determine higher ablation volume compared with regular lithotripsy. However, this technology presents similar characteristics to long pulse Ho:YAG laser, and several studies showed no significant difference between Moses Technology and standard lasers. When used in prostate enucleation, Moses Technology promises to reduce operating time by increasing the efficiency of prostate resection and improve the hemostasis. Moreover, some studies state that it is possible to reduce the HoLEP morbidity. Despite this, the clinical impact of the time reduction remains uncertain and different studies either present relevant limitations or are burdened by significant bias.

Summary
Although Moses effect has been extensively described and characterized, and several studies have been published on the usage of Moses Technology for both laser lithotripsy and laser enucleation of the prostate with Holmium YAG, solid clinical evidence on the real improvement of surgical outcomes is still missing.
Implications of DNA damage repair alterations for the management of prostate cancer
Authors: Lozano Rebeca , Olmos David , Castro Elena 
Published: March 2022

Purpose of review
In this review, we summarize the prevalence of alterations in DNA damage repair (DDR) genes in prostate cancer, their clinical significance, the therapeutic strategies developed to take advantage of the impaired tumour ability to repair DNA and the diagnostic approaches available to identify patients likely to benefit from DDR-targeting agents.

Recent findings
DDR alterations are more frequent in metastatic than in localized prostate cancer and some of them associate with aggressive disease whereas the significance of others remain unclear. The most appropriate management approach for DDR-defective prostate cancer patients is unknown. Clinical trials have demonstrated the efficacy of different poly-ADP ribose polymerase inhibitors (PARPi) to treat metastatic castration-resistant prostate cancer patients with BRCA1/2 alterations, although there may be other DDR alterations that sensitize patients to these drugs. Multiple strategies to target DDR defects are being investigated, including PARPi in combination, platinum-based chemotherapy and immunotherapy, both in earlier and late disease stages. Optimization of molecular testing is paramount for the implementation of precision oncology in prostate cancer.

Summary
Certain DDR defects present in prostate cancer have prognostic and therapeutic implications whereas the significance of other DDR alterations is yet to be elucidated.
The induced membrane technique in animal models: a systematic review
Authors: Sun Hening , Godbout Charles , Hali Kalter , Momic Jovana , Schemitsch Emil H. , Nauth Aaron 
Published: March 2022

Abstract

Objectives:
The induced membrane technique (IMT) is a 2-stage surgical approach that has become increasingly popular to manage bone defects. Preclinical investigations have been conducted to better understand and define several aspects of this technique. This review summarizes the literature regarding the IMT performed in animal models and identifies potential future directions.

Data Sources:
Biosis Citation Index, Ovid Embase, and Ovid MEDLINE databases were searched from inception up to June 23, 2021 for articles related to the IMT.

Study Selection:
Animal studies involving the use of the IMT for segmental defects in long bones were selected. Only full-length original research articles published in English or French were included.

Data Extraction:
Two authors extracted the data from the selected studies and a third author verified the accuracy of the information.

Data Synthesis:
Information concerning the animal model, the surgical procedures, and the outcome measures were recorded for each study and compiled.

Conclusions:
Forty-seven studies were included in this review. Twenty-nine studies (62%) performed both stages of the technique, but only 8 (17%) reported on radiographic union rates explicitly and 5 (11%) included biomechanical testing. A large proportion of the preclinical literature on the IMT has failed to report on radiographic union as an outcome. While studies reporting membrane properties are valuable, they may not provide information that translates into clinical practice or further clinical research if the ultimate outcome of bony healing is not considered. Future animal studies of the IMT should consider this in their study design.
Usefulness of real-time RT-PCR to understand the kinetics of SARS-CoV-2 in blood: a prospective study
Authors: Zurita-Cruz Nelly Daniela , Martín-Ramírez Alexandra , Rodríguez-Serrano Diego Aníbal , González-Álvaro Isidoro , Roy-Vallejo Emilia , De la Cámara Rafael , García-Rodrigo Leticia Fontán , Domingo Laura Cardeñoso 
Published: March 2022

ABSTRACTBackgroundSARS-CoV-2 viral load and kinetics assessed in serial blood samples from hospitalised COVID-19 patients by RT-PCR are poorly understood.MethodsWe conducted an observational, prospective case series study in hospitalised COVID-19 patients. Clinical outcome data (Intensive Care Unit admission and mortality) were collected from all patients until discharge. Viremia was determined longitudinally during hospitalisation, in plasma and serum samples using two commercial and standardised RT-PCR techniques approved for use in diagnosis of SARS-CoV-2. Viral load (copies/mL and log10) was determined with quantitative TaqPath™COVID-19 test.ResultsSARS-CoV-2 viremia was studied in 57 hospitalised COVID-19 patients. Persistent viremia (PV) was defined as two or more quantifiable viral loads detected in blood samples (plasma/serum) during hospitalisation. PV was detected in 16 (28%) patients. All of them, except for one who rapidly progressed to death, cleared viremia during hospitalisation. Poor clinical outcome occurred in 62.5% of patients with PV, while none of the negative patients or those with sporadic viremia presented this outcome (p<0.0001). Viral load was significantly higher in patients with PV than in those with Sporadic Viremia (p<0.05). Patients presented PV for a short period of time: median time from admission was 5 days (Range=2-12) and 4.5 days (Range=2-8) for plasma and serum samples, respectively. Similar results were obtained with all RT-PCR assays for both types of samples.ConclusionsDetection of persistent SARS-CoV-2 viremia, by real time RT-PCR, expressed as viral load over time, could allow identifying hospitalised COVID-19 patients at risk of poor clinical outcome.HighlightsCommercial RT-PCR techniques could be used to monitor SARS-CoV-2 viremia kinetics.SARS-CoV-2 persistent viremia is related with poor outcome in COVID-19 patient.SARS-Cov-2 viremia kinetics could be used as a biomarker of poor prognosis.Plasma samples are the best choice for analysis of SARS-CoV-2 viremia kinetics.
Reconstructing subdistrict-level population denominators in Yemen after six years of armed conflict and forced displacement
Authors: Checchi Francesco , Koum Besson Emilie Sabine 
Published: March 2022

AbstractIntroductionYemen has experienced widespread insecurity since 2014, resulting in large-scale internal displacement. In the absence of reliable vital events registration, we tried to reconstruct the evolution of Yemen’s population between June 2014 and September 2021, at subdistrict (administrative level 3) resolution, while accounting for growth and internal migration.MethodsWe reconstructed subdistrict-month populations starting from June 2014 WorldPop gridded estimates, as a function of assumed birth and death rates, estimated changes in population density, net internal displacement to and from the subdistrict and assumed overlap between internal displacement and WorldPop trends. Available displacement data from the Displacement Tracking Matrix (DTM) project were subjected to extensive cleaning and imputation to resolve missingness, including through machine learning models informed by predictors such as insecurity. We also modelled the evolution of displaced groups before and after assessment points. To represent parameter uncertainty, we complemented the main analysis with sensitivity scenarios.ResultsWe estimated that Yemen’s population rose from about 26.3M to 31.1M during the seven-year analysis period, with considerable pattern differences at sub-national level. We found that some 10 to 14M Yemenis may have been internally displaced during 2015-2016, about five times United Nations estimates. By contrast, we estimated that the internally displaced population had declined to 1-2M by September 2021.ConclusionsThis analysis illustrates approaches to analysing the dynamics of displacement, and the application of different models and data streams to supplement incomplete ground observations. Our findings are subject to limitations related to data quality, model inaccuracy and omission of migration outside Yemen. We recommend adaptations to the DTM project to enable more robust estimation.
VinDr-Mammo: A large-scale benchmark dataset for computer-aided diagnosis in full-field digital mammography
Authors: Nguyen Hieu T. , Nguyen Ha Q. , Pham Hieu H. , Lam Khanh , Le Linh T. , Dao Minh , Vu Van 
Published: March 2022

ABSTRACTMammography, or breast X-ray, is the most widely used imaging modality to detect cancer and other breast diseases. Recent studies have shown that deep learning-based computer-assisted detection and diagnosis (CADe/x) tools have been developed to support physicians and improve the accuracy of interpreting mammography. However, most published datasets of mammography are either limited on sample size or digitalized from screen-film mammography (SFM), hindering the development of CADe/x tools which are developed based on full-field digital mammography (FFDM). To overcome this challenge, we introduce VinDr-Mammo – a new benchmark dataset of FFDM for detecting and diagnosing breast cancer and other diseases in mammography. The dataset consists of 5,000 mammography exams, each of which has four standard views and is double read with disagreement (if any) being resolved by arbitration. It is created for the assessment of Breast Imaging Reporting and Data System (BI-RADS) and density at the breast level. In addition, the dataset also provides the category, location, and BI-RADS assessment of non-benign findings. We make VinDr-Mammo publicly available on https://physionet.org/ as a new imaging resource to promote advances in developing CADe/x tools for breast cancer screening.
Short-term drop in antibody titer after the third dose of SARS-CoV-2 BNT162b2 vaccine in adults
Authors: Herzberg Jonas , Fischer Bastian , Becher Heiko , Becker Ann-Kristin , Honarpisheh Human , Guraya Salman Yousuf , Strate Tim , Knabbe Cornelius 
Published: March 2022

AbstractLittle is known about the longevity of antibodies after a third dose of BNT162b2 (BioNTech/Pfizer). Therefore, the serum antibody levels were evaluated after the third dose of BNT162b2 which dropped significantly within 11 weeks from 4155.59 ± 2373.65 BAU/ml to 2389.10 ± 1433.90 BAU/ml, p-value <0.001 but remained higher than after the second dose.These data underline the positive effect of third dose of BNT162b2 but shows a rapid and significant drop of antibodies within a short span of time.Trial RegistrationThis trial was prospectively registered in the German Clinical Trial Register (DRKS00021270).
Evaluation of the Causal Relationship Between Smoking and Schizophrenia in Asia
Authors: Su Mei-Hsin , Lai Rou-Yi , Lin Yen-Feng , Chen Chia-Yen , Feng Yen-Chen A. , Hsiao Po-Chang , Wang Shi-Heng 
Published: March 2022

AbstractCigarette smoking has been suggested to be associated with the risk of schizophrenia (SCZ) in observational studies. A significant causal effect of smoking on SCZ has been reported in the European population using the Mendelian randomization (MR) approach; however, no evidence of causality was found in participants from East Asia (EAS). Using the Taiwan Biobank (TWBB, sample size up to 79,989), we conducted genome-wide association studies (GWAS) to identify susceptibility loci for smoking behavior, which included the initiation of smoking and the onset age. To maximize the power of genetic discovery in the EAS population, we meta-analyzed GWAS from the TWBB and Biobank Japan (BBJ, sample size up to 165,436) for smoking traits. The GWAS for SCZ was taken from the Asia Psychiatric Genomics Consortium, which included 22,778 cases and 35,362 controls. We performed a two-sample MR to estimate the causality of smoking behavior on SCZ in the EAS population. In TWBB, we identified one novel locus that met genome-wide significance for onset age. In a meta-analysis of TWBB and BBJ, we identified two novel loci for smoking initiation. In MR, a marginal significance was found for the causality of smoking initiation on SCZ (odds ratio (OR) = 4.00, 95% confidence interval (CI) = 0.89–18.01,P= 0.071). Later onset age for smoking was causally associated with a lower risk of SCZ (OR for a per-year increase in onset = 0.96, 95% CI = 0.91–1.01) with a marginal significance (P= 0.098).
Intra-membrane client recognition potentiates the chaperone functions of Calnexin
Authors: Bloemeke Nicolas , Meighen-Berger Kevin , Hitzenberger Manuel , Bach Nina C. , Parr Marina , Coelho Joao P.L. , Frishman Dmitrij , Zacharias Martin , Sieber Stephan A. , Feige Matthias J. 
Published: March 2022

AbstractOne third of the human proteome are membrane proteins. They are particularly vulnerable to misfolding, often requiring assistance by molecular chaperones. Calnexin (CNX), one of the most abundant ER chaperones, plays an important role in membrane protein biogenesis and engages clients via its sugar-binding lectin domain.Using mass spectrometric analyses, we show that Calnexin (CNX) interacts with a large number of non-glycosylated membrane proteins, suggesting additional binding modes. We find that misfolded membrane proteins are preferentially bound by CNX and that CNX uses its single transmembrane domain (TMD) for client recognition. Combining experimental and computational approaches, we systematically dissect signatures for intramembrane client recognition by CNX and identify sequence motifs within the CNX TMD region that mediate client binding. Building on this, we show that intramembrane client binding potentiates the chaperone functions of CNX.Together, this study reveals a widespread role of CNX client recognition in the lipid bilayer, which synergizes with its established lectin-based substrate binding. Molecular chaperones thus can combine different interaction modes to support the biogenesis of the diverse eukaryotic membrane proteome.
Template-based assembly of proteomic short reads forde novoantibody sequencing and repertoire profiling
Authors: Schulte Douwe , Peng Weiwei , Snijder Joost 
Published: March 2022

AbstractAntibodies can target a vast molecular diversity of antigens. This is achieved by generating a complementary diversity of antibody sequences though somatic recombination and hypermutation. A full understanding of the antibody repertoire in health and disease therefore requires dedicatedde novosequencing methods. Next generation cDNA sequencing methods have laid the foundation of our current understanding of the antibody repertoire, but these methods share one major limitation in that they target the antibody-producing B-cells, rather than the functional secreted product in bodily fluids. Mass spectrometry-based methods offer an opportunity to bridge this gap between antibody repertoire profiling and bulk serological assays, as they can access antibody sequence information straight from the secreted polypeptide products. In a step to meeting the challenge of MS-based antibody sequencing, we present a fast and simple software tool (Stitch) to map proteomic short reads to user-defined templates with dedicated features for both monoclonal antibody sequencing and profiling of polyclonal antibody repertoires. We demonstrate the use of Stitch by fully reconstructing 2 monoclonal antibody sequences with >98% accuracy (including I/L assignment); sequencing a Fab from patient serum isolated by reversed-phase LC fractionation against a high background of homologous antibody sequences; sequencing antibody light chains from urine of multiple-myeloma patients; and profiling the IgG repertoire in sera from patients hospitalized with COVID-19. We demonstrate that Stitch assembles a comprehensive overview of the antibody sequences that are represented in the dataset and provides an important first step towards analyzing polyclonal antibodies and repertoire profiling.