bluuebunny/crossref_metadata_2025_split huggingface dataset:
UGM: a more stable procedure for large-scale multiple testing problems, new solutions to identify oncogene
Authors: Liu Chengyou , Zhou Leilei , Wang Yuhe , Tian Shuchang , Zhu Junlin , Qin Hang , Ding Yong , Jiang Hongbing 
Published: December 2019

AbstractVariations of gene expression levels play an important role in tumors. There are numerous methods to identify differentially expressed genes in high-throughput sequencing. Several algorithms endeavor to identify distinctive genetic patterns susceptable to particular diseases. Although these processes have been proved successful, the probability that the number of non-differentially expressed genes measured by false discovery rate (FDR) has a large standard deviation, and the misidentification rate (type I error) grows rapidly when the number of genes to be detected become larger. In this study we developed a new method, Unit Gamma Measurement (UGM), accounting for multiple hypotheses test statistics distribution, which could reduce the dependency problem. Simulated expression profile data and breast cancer RNA-Seq data were utilized to testify the accuracy of UGM. The results show that the number of non-differentially expressed genes identified by the UGM is very close to the real-evidence data, and the UGM also has a smaller standard error, range, quartile range and RMS error. In addition, the UGM can be used to screen many breast cancer-associated genes, such as BRCA1, BRCA2, PTEN, BRIP1, etc., provides better accuracy, robustness and efficiency, the method of identification differentially expressed genes in high-throughput sequencing.
Eumelanin and pheomelanin pigmentation in mollusc shells may be less common than expected: insights from mass spectrometry
Authors: Affenzeller Susanne , Wolkenstein Klaus , Frauendorf Holm , Jackson Daniel J. 
Published: December 2019

Abstract
Background
The geometric patterns that adorn the shells of many phylogenetically disparate molluscan species are comprised of pigments that span the visible spectrum. Although early chemical studies implicated melanin as a commonly employed pigment, surprisingly little evidence generated with more recent and sensitive techniques exists to support these observations.

Results
Here we present the first mass spectrometric investigations for the presence of eumelanin and pheomelanin in 13 different molluscan species from three conchiferan classes: Bivalvia, Cephalopoda and Gastropoda. In the bivalve Mytilus edulis we demonstrate that eumelanin mainly occurs in the outermost, non-mineralised and highly pigmented layer of the shell (often referred to as the periostracum). We also identified eumelanin in the shells of the cephalopod Nautilus pompilius and the marine gastropods Clanculus pharaonius and Steromphala adriatica. In the terrestrial gastropod Cepaea nemoralis we verify the presence of pheomelanin in a mollusc shell for the first time. Surprisingly, in a large number of brown/black coloured shells we did not find any evidence for either type of melanin.

Conclusions
We recommend methods such as high-performance liquid chromatography with mass spectrometric detection for the analysis of complex biological samples to avoid potential false-positive identification of melanin. Our results imply that many molluscan species employ as yet unidentified pigments to pattern their shells. This has implications for our understanding of how molluscs evolved the ability to pigment and pattern their shells, and for the identification of the molecular mechanisms that regulate these processes.
Individualized feedback to change multiple gait deficits in chronic stroke
Authors: Day Kevin A. , Cherry-Allen Kendra M. , Bastian Amy J. 
Published: December 2019

AbstractBackgroundWalking deficits in people post-stroke are often multiple and idiosyncratic in nature. Limited patient and therapist resources necessitate prioritization of deficits such that some may be left unaddressed. More efficient delivery of therapy may alleviate this challenge. Here, we look to determine the utility of a novel principal component-based visual feedback system that targets multiple, patient-specific features of gait in people post-stroke.MethodsTen individuals with stroke received two sessions of visual feedback to attain a walking goal. This goal consisted of bilateral knee and hip joint angles of a typical ‘healthy’ walking pattern. The feedback system uses principal component analysis (PCA) to algorithmically weight each of the input features so that participants received one stream of performance feedback. In the first session, participants had to explore different patterns to achieve the goal, and in the second session they were informed of the goal walking pattern. Ten healthy, age-matched individuals received the same paradigm, but with a hemiparetic goal (i.e. to produce the pattern of an exemplar stroke participant). This was to distinguish the extent to which performance limitations in stroke were due neurological injury or the PCA based visual feedback itself.ResultsPrincipal component-based visual feedback can differentially bias multiple features of walking toward a prescribed goal. On average, individuals with stroke typically improved performance via increased paretic knee and hip flexion, and did not perform better with explicit instruction. In contrast, healthy people performed better (i.e. could produce the desired exemplar stroke pattern) in both sessions, and were best with explicit instruction. Importantly, the feedback for stroke participants accommodated a heterogeneous set of walking deficits by individually weighting each feature based on baseline walking.ConclusionsPeople with and without stroke are able to use this novel visual feedback to train multiple, specific features of gait. Important for stroke, the PCA feedback allowed for targeting of patient-specific deficits. This feedback is flexible to any feature of walking in any plane of movement, thus providing a potential tool for therapists to simultaneously target multiple aberrant features of gait.
Inhibition effects of patchouli alcohol against influenza a virus through targeting cellular PI3K/Akt and ERK/MAPK signaling pathways
Authors: Yu Yunjia , Zhang Yang , Wang Shuyao , Liu Wei , Hao Cui , Wang Wei 
Published: December 2019

AbstractBackgroundPatchouli alcohol (PA) is a tricyclic sesquiterpene extracted fromPogostemonis Herba, which is a traditional Chinese medicine used for therapy of inflammatory diseases. Recent studies have shown that PA has various pharmacological activities, including anti-bacterial and anti-viral effects.MethodsIn this study, the anti-influenza virus (IAV) activities and mechanisms were investigated both in vitro and in vivo. The inhibitory effects of PA against IAV in vitro were evaluated by plaque assay and immunofluorescence assay. The neuraminidase inhibition assay, hemagglutination inhibition (HI) assay, and western blot assay were used to explore the anti-viral mechanisms. The anti-IAV activities in vivo were determined by mice pneumonia model and HE staining.ResultsThe results showed that PA significantly inhibited different IAV strains multiplication in vitro, and may block IAV infection through inactivating virus particles directly and interfering with some early stages after virus adsorption. Cellular PI3K/Akt and ERK/MAPK signaling pathways may be involved in the anti-IAV actions of PA. Intranasal administration of PA markedly improved mice survival and attenuated pneumonia symptoms in IAV infected mice, comparable to the effects of Oseltamivir.ConclusionsTherefore, Patchouli alcohol has the potential to be developed into a novel anti-IAV agent in the future.
Can pulsatile CSF flow across the cerebral aqueduct cause ventriculomegaly? A prospective study of patients with communicating hydrocephalus
Authors: Holmlund P. , Qvarlander S. , Malm J. , Eklund A. 
Published: December 2019

Abstract
Background
Communicating hydrocephalus is a disease where the cerebral ventricles are enlarged. It is characterized by the absence of detectable cerebrospinal fluid (CSF) outflow obstructions and often with increased CSF pulsatility measured in the cerebral aqueduct (CA). We hypothesize that the cardiac-related pulsatile flow over the CA, with fast systolic outflow and slow diastolic inflow, can generate net pressure effects that could source the ventriculomegaly in these patients. This would require a non-zero cardiac cycle averaged net pressure difference (ΔPnet) over the CA, with higher average pressure in the lateral and third ventricles.

Methods
We tested the hypothesis by calculating ΔPnet across the CA using computational fluid dynamics based on prospectively collected high-resolution structural (FIESTA-C, resolution 0.39 × 0.39 × 0.3 mm3) and velocimetric (2D-PCMRI, in-plane resolution 0.35 × 0.35 mm2) MRI-data from 30 patients investigated for communicating hydrocephalus.

Results
The ΔPnet due to CSF pulsations was non-zero for the study group (p = 0.03) with a magnitude of 0.2 ± 0.4 Pa (0.001 ± 0.003 mmHg), with higher pressure in the third ventricle. The maximum pressure difference over the cardiac cycle ΔPmax was 20.3 ± 11.8 Pa and occurred during systole. A generalized linear model verified an association between ΔPnet and CA cross-sectional area (p = 0.01) and flow asymmetry, described by the ratio of maximum inflow/outflow (p = 0.04), but not for aqueductal stroke volume (p = 0.35).

Conclusions
The results supported the hypothesis with respect to the direction of ΔPnet, although the magnitude was low. Thus, although the pulsations may generate a pressure difference across the CA it is likely too small to explain the ventriculomegaly in communicating hydrocephalus.
Fluctuating light experiments and semi-automated plant phenotyping enabled by self-built growth racks and simple upgrades to the IMAGING-PAM
Authors: Schneider Dominik , Lopez Laura S. , Li Meng , Crawford Joseph D. , Kirchhoff Helmut , Kunz Hans-Henning 
Published: December 2019

Abstract
Background
Over the last years, several plant science labs have started to employ fluctuating growth light conditions to simulate natural light regimes more closely. Many plant mutants reveal quantifiable effects under fluctuating light despite being indistinguishable from wild-type plants under standard constant light. Moreover, many subtle plant phenotypes become intensified and thus can be studied in more detail. This observation has caused a paradigm shift within the photosynthesis research community and an increasing number of scientists are interested in using fluctuating light growth conditions. However, high installation costs for commercial controllable LED setups as well as costly phenotyping equipment can make it hard for small academic groups to compete in this emerging field.

Results
We show a simple do-it-yourself approach to enable fluctuating light growth experiments. Our results using previously published fluctuating light sensitive mutants, stn7 and pgr5, confirm that our low-cost setup yields similar results as top-prized commercial growth regimes. Moreover, we show how we increased the throughput of our Walz IMAGING-PAM, also found in many other departments around the world. We have designed a Python and R-based open source toolkit that allows for semi-automated sample segmentation and data analysis thereby reducing the processing bottleneck of large experimental datasets. We provide detailed instructions on how to build and functionally test each setup.

Conclusions
With material costs well below USD$1000, it is possible to setup a fluctuating light rack including a constant light control shelf for comparison. This allows more scientists to perform experiments closer to natural light conditions and contribute to an emerging research field. A small addition to the IMAGING-PAM hardware not only increases sample throughput but also enables larger-scale plant phenotyping with automated data analysis.
Mechanisms for the temporal regulation of substrate ubiquitination by the anaphase-promoting complex/cyclosome
Authors: Bansal Shivangee , Tiwari Swati 
Published: December 2019

AbstractThe anaphase-promoting complex/cyclosome (APC/C) is a multi-subunit, multifunctional ubiquitin ligase that controls the temporal degradation of numerous cell cycle regulatory proteins to direct the unidirectional cell cycle phases. Several different mechanisms contribute to ensure the correct order of substrate modification by the APC/C complex. Recent advances in biochemical, biophysical and structural studies of APC/C have provided a deep mechanistic insight into the working of this complex ubiquitin ligase. This complex displays remarkable conformational flexibility in response to various binding partners and post-translational modifications, which together regulate substrate selection and catalysis of APC/C. Apart from this, various features and modifications of the substrates also influence their recognition and affinity to APC/C complex. Ultimately, temporal degradation of substrates depends on the kind of ubiquitin modification received, the processivity of APC/C, and other extrinsic mechanisms. This review discusses our current understanding of various intrinsic and extrinsic mechanisms responsible for ‘substrate ordering’ by the APC/C complex.
The essentiality landscape of cell cycle related genes in human pluripotent and cancer cells
Authors: Viner-Breuer Ruth , Yilmaz Atilgan , Benvenisty Nissim , Goldberg Michal 
Published: December 2019

Abstract
Background
Cell cycle regulation is a complex system consisting of growth-promoting and growth-restricting mechanisms, whose coordinated activity is vital for proper division and propagation. Alterations in this regulation may lead to uncontrolled proliferation and genomic instability, triggering carcinogenesis. Here, we conducted a comprehensive bioinformatic analysis of cell cycle-related genes using data from CRISPR/Cas9 loss-of-function screens performed in four cancer cell lines and in human embryonic stem cells (hESCs).

Results
Cell cycle genes, and in particular S phase and checkpoint genes, are highly essential for the growth of cancer and pluripotent cells. However, checkpoint genes are also found to underlie the differences between the cell cycle features of these cell types. Interestingly, while growth-promoting cell cycle genes overlap considerably between cancer and stem cells, growth-restricting cell cycle genes are completely distinct. Moreover, growth-restricting genes are consistently less frequent in cancer cells than in hESCs. Here we show that most of these genes are regulated by the tumor suppressor gene TP53, which is mutated in most cancer cells. Therefore, the growth-restriction system in cancer cells lacks important factors and does not function properly. Intriguingly, M phase genes are specifically essential for the growth of hESCs and are highly abundant among hESC-enriched genes.

Conclusions
Our results highlight the differences in cell cycle regulation between cell types and emphasize the importance of conducting cell cycle studies in cells with intact genomes, in order to obtain an authentic representation of the genetic features of the cell cycle.
“The role as a champion is to not only monitor but to speak out and to educate”: the contradictory roles of hand hygiene champions
Authors: Goedken Cassie Cunningham , Livorsi Daniel J. , Sauder Michael , Vander Weg Mark W. , Chasco Emily E. , Chang Nai-Chung , Perencevich Eli , Reisinger Heather Schacht 
Published: December 2019

AbstractBackgroundImplementation science experts define champions as “supporting, marketing, and driving through an implementation, overcoming indifference or resistance that the intervention may provoke in an organization.” Many hospitals use designated clinical champions—often called “hand hygiene (HH) champions”—typically to improve hand hygiene compliance. We conducted an ethnographic examination of how infection control teams in the Veterans Health Administration (VHA) use the term “HH champion” and how they define the role.MethodsAn ethnographic study was conducted with infection control teams and frontline staff directly involved with hand hygiene across 10 geographically dispersed VHA facilities in the USA. Individual and group semi-structured interviews were conducted with hospital epidemiologists, infection preventionists, multi-drug-resistant organism (MDRO) program coordinators, and quality improvement specialists and frontline staff from June 2014 to September 2017. The team coded the transcripts using thematic content analysis content based on a codebook composed of inductive and deductive themes.ResultsA total of 173 healthcare workers participated in interviews from the 10 VHA facilities. All hand hygiene programs at each facility used the term HH champion to define a core element of their hand hygiene programs. While most described the role of HH champions as providing peer-to-peer coaching, delivering formal and informal education, and promoting hand hygiene, a majority also included hand hygiene surveillance. This conflation of implementation strategies led to contradictory responsibilities for HH champions. Participants described additional barriers to the role of HH champions, including competing priorities, staffing hierarchies, and turnover in the role.ConclusionsHealthcare systems should consider narrowly defining the role of the HH champion as a dedicated individual whose mission is to overcome resistance and improve hand hygiene compliance—and differentiate it from the role of a “compliance auditor.” Returning to the traditional application of the implementation strategy may lead to overall improvements in hand hygiene and reduction of the transmission of healthcare-acquired infections.
Prediction of VMAT delivery accuracy with textural features calculated from fluence maps
Authors: Park Jong Min , Kim Jung-in , Park So-Yeon 
Published: December 2019

Abstract
Background
Comprehensively textural feature performance test from volumetric modulated arc therapy (VMAT) fluences to predict plan delivery accuracy.

Methods
A total of 240 VMAT plans for various treatment sites were analyzed, with Trilogy and TrueBeam STx systems. Fluence maps superposed fluences at each control point per plan. The textural features were the angular second moment (ASM), inverse difference moment (IDM), contrast, variance, correlation, and entropy, calculated from fluence maps using three displacement distances. Correlation analysis of textural feature performance as predictors of VMAT delivery accuracy used global gamma passing rates with MapCHECK2 and ArcCHECK dosimeters, and mechanical delivery errors calculated from machine log files.

Results
Spearman’s rank correlation coefficients (r) of the ASM (d = 10) to the gamma passing rates with 1%/2 mm using the MapCHECK2 were 0.358 and 0.519, respectively (p <  0.001). For the ArcCHECK, they were 0.273 (p = 0.001) and 0.259 (p = 0.009), respectively. The r-values of the ASM (d = 10) to the Trilogy and TrueBeam STx MLC errors were − 0.843 and − 0.859, respectively (p <  0.001), and those to the MU delivery errors were − 0.482 and − 0.589, respectively (p <  0.001). The ASM (d = 10) showed better performance in predicting VMAT delivery accuracy.

Conclusions
The ASM (d = 10) calculated from VMAT plan fluence maps were strongly correlated with global gamma passing rates and MLC delivery errors, and can predict VMAT delivery accuracy.
Anterior percutaneous full-endoscopic transcorporeal decompression of the spinal cord for single-segment cervical spondylotic myelopathy: The technical interpretation and 2 years of clinical follow-up
Authors: Kong Weijun , Xin Zhijun , Du Qian , Cao Guangru , Liao Wenbo 
Published: December 2019

Abstract
Background
ACDF is the standard procedure for treatment of cervical spondylotic myelopathy (CSM), but a long-term follow-up has been revealed some associated complications of swallowing discomfort, displacement of the fusion device, and accelerated degeneration of the adjacent segment.

Objective
To evaluate the clinical outcomes of anterior percutaneous full-endoscopic transcorporeal decompression of the spinal cord (APFETDSC) for single-segment CSM and to analyze the clinical efficacy, surgical characteristics, and complication prevention.

Methods
A total of 32 patients who underwent APFETDSC for single-segment CSM from Aug. 2015 to Apr. 2017 were reviewed. Operating time, time of walking out of bed postoperation, length of hospitalization, complications, neck pain visual analog scale (VAS), and Japanese Orthopaedic Association Score (JOA) were evaluated. Measurement of intervertebral height (HI) of surgical segments on cervical neutral X-ray, Harrison’s method was used to measure cervical spine angle (CSA).

Results
The operation time was 103.3 ± 12.95 min, time of walking out of bed after surgery was 19.81 ± 4.603 h, the length of postoperative hospital stay was 57.48 ± 19.48 h. The postoperative neck pain VAS and JOA were significantly improved compared with preoperation(p < 0.001). The postoperative HI was statistical significance decreased compared with preoperation(p < 0.001), but the HI reduction was less than 0.5 mm, without adverse clinical symptoms. The postoperative CSA was significantly improved compared with preoperative(p < 0.001). The excellent and good rate was 87.5%, and the JOA improvement rate was 75.52 ± 11.11%. There was no cervical instability, vertebral fracture, wound infection, and other complications.

Conclusions
APFETDSC is a safe and effective minimally invasive technique with small auxiliary injuries for single-segment CSM while avoiding the sequelae of ACDF. Its short-term clinical efficacy was good and no significant effect on cervical stability.