bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transjugular intrahepatic portosystemic shunt for patients with liver cirrhosis: survey evaluating indications, standardization of procedures and anticoagulation in 43 German hospitals
Authors: Steib Christian J. , Li Hanwei , Zhang Jiang , Mayerle Julia , Ricke Jens , Gerbes Alexander L. , Meyer Carsten , Zipprich Alexander , Trebicka Jonel 
Published: December 2019

Objectives
Transjugular intrahepatic portosystemic shunt (TIPS) insertion is an established treatment to lower portal pressure. There are no obligatory evidence-based recommendations addressing procedure and anticoagulation. Therefore, a survey was performed to establish current practice at different German hospitals.

Methods
A three-page survey was sent out via postal mail to 76 different hospitals addressing the topics indication, contraindication, follow-up and anticoagulation.

Results
Forty-three hospitals completed the survey: the median number of TIPS/year was 28.6 ± 23. Ascites and hydrothorax were announced as the main indications. Bilirubin levels above 5 mg/dl, hepatic encephalopathy and cardiac disease were considered as absolute contraindications in most hospitals, but age was not. The biggest variations were reported with regard to anticoagulation after TIPS procedure. Four hospitals never used any anticoagulation; most hospitals reported the use of low molecular weight heparins for a period of days up to 4 weeks. But also aspirin or clopidogrel was used after TIPS insertion in eight different hospitals. Additionally, the standards for follow-up after TIPS insertion were different in the hospitals.

Conclusions
There is no consensus how to handle indication, contraindications and anticoagulation after the TIPS procedure. A national and international consensus is warranted to improve the outcome of TIPS patients and reduce secondary complications. In addition to compare results and efficacy in the future standard operation procedures as proposed here need to be put in place.
Fully Covered Self-Expandable Metal Stens eliminate surgical repair requirement in both endoscopic sphincterotomy and precut sphincterotomy-related perforation (with video)
Authors: Parlak Erkan , Koksal Aydin Seref , Eminler Ahmet Tarik , Ercan Metin , Toka Bilal , Karaman Kerem , Uslan Mustafa Ihsan 
Published: December 2019

Objective
Endoscopic retrograde cholangiopancreatography (ERCP)-related perforations occur in 0.3–0.6% of patients. The treatment of retroperitoneal paravaterian perforations (type II), which develop during endoscopic sphincterotomy or precut sphincterotomy, remains a matter of debate. We aimed to evaluate the efficacy of fully covered self expandable metal stent (Fc-SEMS) placement in the treatment of type II perforations.

Methods
The study was conducted in a tertiary ERCP reference center of Turkey between December 2013 and June 2016. Patients with type II ERCP-related perforation constituted the study group. Type II perforations were treated by insertion of an Fc-SEMS (10 mm × 60 mm) during the ERCP procedure or intraoperatively by surgery-endoscopy rendezvous technique, if biliary cannulation could not be achieved.

Results
A total of 2689 ERCPs were performed. ERCP-related perforation was observed in 12 procedures (0.4%). Eight patients had Stapfer type II perforations, which developed during endoscopic sphincterotomy in seven patients and precut sphincterotomy in one patient. Fc-SEMSs were inserted during the ERCP procedure in seven patients and intraoperatively by surgery-endoscopy rendezvous technique in one patient. None of the patients developed fever, hemodynamic instability, or peritoneal signs. Stents were removed after a median duration of 9 (3–14) days. All of the patients were uneventfully discharged after an average hospital length of stay of median 5 (1–9) days.

Conclusion
Fc-SEMSs are highly effective in the nonoperative treatment of type II perforations and their intraoperative insertion in patients with unsuccessful cannulation may facilitate surgery by eliminating the need for duodenum repair surgery.
Heme is involved in the systemic inflammatory response following radiofrequency ablation of hepatic hemangiomas
Authors: Yang Xu , Liu Jun , Yang Meng-Meng , Wang Shao-Hong , Xu Li , Ke Shan , Ding Xue-Mei , Sun Wen-Bing , Gao Jun 
Published: December 2019

Objective
Radiofrequency ablation (RFA) is an effective and minimally invasive treatment for managing hepatic hemangiomas. Systemic inflammatory response syndrome (SIRS) often occurs with hemoglobinuria, and its underlying pathophysiological mechanism is unknown. Heme can trigger inflammation by inducing the generation of reactive oxygen species (ROS) and the production of inflammatory mediators. We therefore investigated whether circulating heme is involved in SIRS following RFA of hepatic hemangiomas.

Methods
We enrolled 65 patients with hepatic hemangioma who underwent RFA. Serum concentrations of free heme, ROS, and tumor necrosis factor α (TNF-α) were measured after RFA. Univariate analysis and a multivariate binary logistic regression model were used to evaluate the contribution of 17 risk factors for SIRS after RFA.

Results
Fifty-nine (59/65, 90.8%) patients developed hemoglobinuria, among which 25 (25/59, 42.4%) experienced SIRS shortly after RFA. In the SIRS group, the serum concentrations of heme, ROS, and TNF-α were immediately elevated after RFA compared with baseline and slowly regained their normal levels 3 days after RFA. Moreover, the concentrations of circulating heme significantly correlated with those of ROS (r = 0.805, P < 0.001) and TNF-α (r = 0.797, P < 0.001). Multivariate analysis showed that the volume of hemangioma [odds ratio (OR) = 1.293, P = 0.031], time of ablation (OR = 1.194, P = 0.029) as well as the concentrations of heme (OR = 1.430, P = 0.017), ROS (OR = 1.251, P = 0.031), and TNF-α (OR = 1.309, P = 0.032) were significantly associated with SIRS.

Conclusion
Circulating heme was associated with the induction of ROS and the production of TNF-α, which may contribute to the induction of SIRS following RFA of hepatic hemangiomas.
Serial clinical observation for management of newborns at risk of early-onset sepsis
Authors: Berardi Alberto , Bedetti Luca , Spada Caterina , Lucaccioni Laura , Frymoyer Adam 
Published: December 2019

Purpose of review
Current management approaches for asymptomatic neonates at risk of early onset sepsis remain controversial. Strategies based entirely on clinical observation (SCO, serial clinical observation) have gained consensus.

Recent findings
We briefly compare different strategies for managing asymptomatic newborns suggested in four high-income countries. Then this review details the existing differences in carrying out the SCO in the United Kingdom, the USA, and Italy; the experiences from the studies performed using the SCO; and open questions regarding this strategy. Advantages and limitations of SCO are also discussed. There is a need to assess which symptoms at birth are more predictive of early onset sepsis and therefore require immediate interventions versus those symptoms that can be monitored and re-evaluated.

Summary
SCO strategy may require changes in the processes of newborn care at birthing centers. Nonetheless, SCO is safe and is associated with fewer laboratory evaluations and unnecessary antibiotics. Thoughtful and thorough practices related to the care of all newborns will benefit any birthing centre.

Video abstract

http://links.lww.com/MOP/A40.
Rotavirus vaccination in the neonatal intensive care units: where are we? A rapid review of recent evidence
Authors: Sicard Mélanie , Bryant Kristina , Muller Martha L. , Quach Caroline 
Published: December 2019

Purpose of review
Rotavirus is a leading cause of viral acute gastroenteritis in infants. Neonates hospitalized in neonatal intensive care units (NICUs) are at risk of rotavirus infections with severe outcomes. The administration of rotavirus vaccines is only recommended, in the United States and Canada, upon discharge from the NICU despite rotavirus vaccines being proven well tolerated and effective in these populations, because of risks of live-attenuated vaccine administration in immunocompromised patients and theoretical risks of rotavirus vaccine strains shedding and transmission.
We aimed to summarize recent evidence regarding rotavirus vaccine administration in the NICU setting and safety of rotavirus vaccines in preterm infants.

Methods
We conducted a rapid review of the literature from the past 10 years, searching Medline and Embase, including all study types except reviews, reporting on rotavirus vaccines 1 and 5; NICU setting; shedding or transmission; safety in preterm. One reviewer performed data extraction and quality assessment.

Recent findings
Thirty-one articles were analyzed. Vaccine-derived virus shedding following rotavirus vaccines existed for nearly all infants, mostly during the first week after dose 1, but with rare transmission only described in the household setting. No case of transmission in the NICU was reported. Adverse events were mild to moderate, occurring in 10–60% of vaccinated infants. Extreme premature infants or those with underlying gastrointestinal failure requiring surgery presented with more severe adverse events.

Summary
Recommendations regarding rotavirus vaccine administration in the NICU should be reassessed in light of the relative safety and absence of transmission of rotavirus vaccine strains in the NICU.
Sudden Death Due to Calcifying Pseudoneoplasm of the Neuraxis
Authors: Conway Kyle S. , Jentzen Jeffrey , Pratt Drew , Camelo-Piragua Sandra 
Published: December 2019

AbstractWe present a case of a 22-year-old man who died unexpectedly after a seizure due to a previously undiagnosed calcifying pseudoneoplasm of the neuraxis (CAPNON). Calcifying pseudoneoplasm of the neuraxis is a rare entity, and this is, to our knowledge, the first described case of sudden death due to CAPNON. Sudden death due to undiagnosed central nervous system mass lesions is rare, and most cases are attributable to hemorrhage, hydrocephalus, or increased intracranial pressure due to mass effect. Seizure is a rare cause of sudden death due to central nervous system mass lesions. This case highlights that mass lesions may cause sudden death due to seizure, even without other pathologic evidence of a cause of death, such as hemorrhage or edema. Furthermore, benign, reactive, and low-grade mass lesions may cause sudden death due to seizure. Seizure should remain in the autopsy differential as a cause of death, even where there is no pathologically evident mechanism by which a mass lesion caused death.
Strategy in wheat-Fusariumdual-genome RNA-seq data processing
Authors: Liu Ziying , Li Yifeng , Pan Youlian , Wang Lipu , Ouellet Therese , Fobert Pierre 
Published: December 2019

AbstractIn RNA-seq data processing, short read alignments are usually of one species against its own genome; however, in plant-microbe interaction systems, reads from both host and pathogen samples are blended together. In contrast to single-genome, both pathogen and host reference genomes are involved in the alignment process. In such circumstances, the order of alignment to the host, the pathogen, or simultaneously to both genomes results in differences in read counts of certain genes, especially at the advanced infection stage. It is crucial to have an appropriate strategy for aligning the reads to their respective genomes, yet the existing strategies of either sequential or parallel alignment become a problem when mapping mixed reads to their corresponding reference genomes. The challenge lies in the determination of which reads belong to which species, especially when homology exists between the two genomes.This study proposes a combo-genome alignment strategy after comparing three alignment scenarios. Simulation results demonstrated that the degree of discrepancy in the results is correlated with phylogenetic distance of the two species in the mixture which was attributable to the extent of homology between the two genomes involved. This correlation was also found in the analysis using two real RNA-seq datasets ofFusarium-challenged wheat plants. Comparisons of the three RNA-seq processing strategies on three simulation datasets and two realFusarium-infected wheat datasets showed that an alignment to a combo-genome, consisting of both host and pathogen genomes, improves mapping quality as compared to sequential alignment procedures.
Sequence Comparison without Alignment: TheSpaMapproaches
Authors: Morgenstern Burkhard 
Published: December 2019

AbstractSequence alignment is at the heart of DNA and protein sequence analysis. For the data volumes that are nowadays produced by massively parallel sequencing technologies, however, pairwise and multiple alignment methods have become too slow for many data-analysis tasks. Therefore, fast alignment-free approaches to sequence comparison have become popular in recent years. Most of these approaches are based onword frequencies, for words of a fixed length, or on word-matchingstatistics. Other approaches are based on the length ofmaximal word matches. While these methods are very fast, most of them are based on ad-hoc measures of sequences similarity or dissimilarity that are often hard to interpret. In this review article, I describe a number of alignment-free methods that we developed in recent years. Our approaches are based onspaced word matches (‘SpaM’), i.e. on inexact word matches, that are allowed to contain mismatches at certain pre-defined positions. Unlike most previous alignment-free approaches, our approaches are able to accurately estimate phylogenetic distances between DNA or protein sequences based on stochastic models of molecular evolution.
F1000ResearchTMATCH: A New Algorithm for Protein Alignments using amino-acid hydrophobicities
Authors: Cavanaugh David , Chittur Krishnan 
Published: December 2019

AbstractThe identification of proteins of similar structure using sequence alignment is an important problem in bioinformatics. We decribe TMATCH, a basic dynamic programming alignment algorithm which can rapidly identify proteins of similar structure from a database. TMATCH was developed to utilize an optimal hydrophobicity metric for alignments traceable to fundamental properties of amino-acids. Standard alignment algorithms use affine gap penalties as contrasted with the TMATCH algorithm adaptation of local alignment score reinforcement of favorable diagonal paths (transitions) and punishment of unfavorable transitions paired with fixed gap opening penalties. The TMATCH algorithm is especially designed to take advantage of the extra information available within the hydrophobicity scale to detect homologies, as opposed to the probabilities derived from raw percent identities.
Systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes
Authors: Garge Riddhiman K. , Laurent Jon M. , Kachroo Aashiq H. , Marcotte Edward M. 
Published: December 2019

AbstractMany gene families have been expanded by gene duplications along the human lineage, relative to ancestral opisthokonts, but the extent to which the duplicated genes function similarly is understudied. Here, we focused on structural cytoskeletal genes involved in critical cellular processes including chromosome segregation, macromolecular transport, and cell shape maintenance. To determine functional redundancy and divergence of duplicated human genes, we systematically humanized the yeast actin, myosin, tubulin, and septin genes, testing ∼85% of human cytoskeletal genes across 7 gene families for their ability to complement a growth defect induced by deletion of the corresponding yeast ortholog. In 5 of 7 families—all but α-tubulin and light myosin, we found at least one human gene capable of complementing loss of the yeast gene. Despite rescuing growth defects, we observed differential abilities of human genes to rescue cell morphology, meiosis, and mating defects. By comparing phenotypes of humanized strains with deletion phenotypes of their interaction partners, we identify instances of human genes in the actin and septin families capable of carrying out essential functions, but apparently failing to interact with components of the yeast cytoskeleton, thus leading to abnormal cell morphologies. Overall, we show that duplicated human cytoskeletal genes appear to have diverged such that only a few human genes within each family are capable of replacing the essential roles of their yeast orthologs. The resulting yeast strains with humanized cytoskeletal components now provide surrogate platforms to characterize human genes in simplified eukaryotic contexts.
Separable functions of Tof1/Timeless in intra-S-checkpoint signalling, replisome stability and DNA topological stress
Authors: Westhorpe Rose , Keszthelyi Andrea , Minchell Nicola E. , Jones David , Baxter Jonathan 
Published: December 2019

AbstractThe highly conserved Tof1/Timeless proteins minimise replication stress and promote normal DNA replication. They are required to mediate the DNA replication checkpoint (DRC), the stable pausing of forks at protein fork blocks, the coupling of DNA helicase and polymerase functions during replication stress (RS) and the preferential resolution of DNA topological stress ahead of the fork. Here we demonstrate that the roles of theSaccharomyces cerevisiaeTimeless protein Tof1 in DRC signalling and resolution of DNA topological stress require distinct N and C terminal regions of the protein, whereas the other functions of Tof1 are closely linked to the stable interaction between Tof1 and its constitutive binding partner Csm3/Tipin. By separating the role of Tof1 in DRC from fork stabilisation and coupling, we show that Tof1 has distinct activities in checkpoint activation and replisome stability to ensure the viable completion of DNA replication following replication stress.
ABHD4-dependent developmental anoikis protects the prenatal brain from pathological insults
Authors: László Zsófia I. , Lele Zsolt , Zöldi Miklós , Miczán Vivien , Mógor Fruzsina , Simon Gabriel M. , Mackie Ken , Kacskovics Imre , Cravatt Benjamin F. , Katona István 
Published: December 2019

AbstractIn light of the astronomical number of cell divisions taking place in restricted neurogenic niches, brain malformations caused by ectopic proliferation of misplaced progenitor cells are surprisingly rare. Here, we show that a process we term developmental anoikis distinguishes the abnormal detachment of progenitor cells from the normal delamination of daughter neuroblasts in the developing mouse neocortex. By usingin vivogain-of-function, loss-of-function, and rescue manipulations together with correlated confocal and super-resolution imaging, we identify the endocannabinoid-metabolizing enzyme abhydrolase domain containing 4 (ABHD4) as an essential mediator for the elimination of abnormally detached cells. Consequently, rapid ABHD4 downregulation is necessary for delaminated daughter neuroblasts to escape from anoikis. Moreover, ABHD4 is required for fetal alcohol-induced apoptosis, but not for the well-established form of developmentally controlled programmed cell death. These results suggest that ABHD4-mediated developmental anoikis specifically protects the embryonic brain from the consequences of sporadic delamination errors and teratogenic insults.
Mechanics of multi-centrosomal clustering in bipolar mitotic spindles
Authors: Chatterjee S , Sarkar A , Zhu J , Khodjakov A , Mogilner A , Paul R 
Published: December 2019

ABSTRACTTo segregate chromosomes in mitosis, cells assemble mitotic spindle, a molecular machine with centrosomes at two opposing cell poles and chromosomes at the equator. Microtubules and molecular motors connect the poles to kinetochores, specialized protein assemblies on the centromere regions of the chromosomes. Bipolarity of the spindle is crucial for the proper cell division, and two centrosomes in animal cells naturally become two spindle poles. Cancer cells are often multi-centrosomal, yet they are able to assemble bipolar spindles by clustering centrosomes into two spindle poles. Mechanisms of this clustering are debated. In this study, we computationally screen effective forces between a) centrosomes, b) centrosomes and kineto-chores, c) centrosomes and chromosome arms, d) centrosomes and cell cortex, to understand mechanics that determines three-dimensional spindle architecture. To do this, we use stochastic Monte Carlo search for stable mechanical equilibria in effective energy landscape of the spindle. We find that the following conditions have to be met to robustly assemble the bipolar spindle in a multi-centrosomal cell: 1) strengths of centrosomes’ attraction to each other and to the cell cortex have to be proportional to each other; 2) strengths of centrosomes’ attraction to kinetochores and repulsion from the chromosome arms have to be proportional to each other. We also find that three other spindle configurations emerge if these conditions are not met: a) collapsed, b) monopolar, c) multipolar spindles, and the computational screen reveal mechanical conditions for these abnormal spindles.Significance statementTo segregate chromosomes, cells assemble bipolar mitotic spindle. Multiple mechanical forces generated by microtubules and molecular motors in the spindle govern the spindle architecture, but it is unclear what force balances support the bipolarity of the spindle. This problem is especially difficult and important in cancer cells, which often have multiple centrosomes that somehow are able to cluster into two spindle poles. By using stochastic energy minimization in an effective energy landscape of the spindle and computationally screening forces, we find mechanical conditions for mono-, multi- and bi-polar spindles. We predict how microtubule and motor parameters have to be regulated in mitosis in multi-centrosomal cells.
Combating police corruption in Japan: new challenges ahead?
Authors: Oyamada Eiji 
Published: December 2019

PurposeThe purpose of this paper is to analyze Japanese police corruption and assess the effectiveness of the police reforms to minimize it.Design/methodology/approachThis paper focusses on police corruption in Japan by analyzing its causes and evaluating the effectiveness of measures to prevent it. The paper concludes with some recommendations for minimizing police corruption in Japan.FindingsEven though recent preventive measures in Japan initiated through police reforms have reduced opportunities for police corruption, it is still necessary to improve public trust in the police. The Japanese police do not initiate anti-corruption measures, but focus instead on prevention through ethics training and reliance on stringent regulations. Fostering a civil society coalition for monitoring police corruption, conducting public perceptions surveys of corruption and bringing police corruption studies into academic discussions are tools for tackling police corruption.Originality/valueThis paper will be useful for scholars, policy-makers and anti-corruption practitioners interested in learning how the Japanese police prevent corruption.