bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient-Generated Actigraphy Data as a Novel Outcomes Instrument in Carpal Tunnel Syndrome
Authors: McMahon Heather A. , Heineman John T. , DeGeorge Brent R. 
Published: February 2020

Background
Currently, we lack objective measures to quantify outcomes in carpal tunnel syndrome. Instead, surgeons rely on patient-reported outcomes measures (PROMs) to assess the effect of carpal tunnel release (CTR). We assessed the validity and reliability of wearable activity monitors to objectively characterize the functional and sleep impact of CTR. We hypothesized that actigraphy could detect changes in sleep and activity and would demonstrate short-term impairment due the operative procedure.

Methods
This pilot, prospective, cohort study compared validated PROMS with actigraphy data obtained via wearable activity monitors (ActiGraph Link; ActiGraph Corp, Pensacola, Fla). Subjects completed baseline questionnaires and wore their device for 1 week preoperatively as a baseline. Subjects then underwent open CTR, wearing actigraphy devices for 4 weeks and completing questionnaires at 2 and 4 weeks postoperatively. Preintervention and postintervention data were compared using paired-sample t test. The Patient-Reported Outcomes Measurement Information System (PROMIS) questionnaire data were analyzed in accordance with published PROMIS scoring manuals and raw scores were converted to standardized T scores.

Results
Twenty subjects (5 males, 15 females) with moderate or severe carpal tunnel syndrome were enrolled. The mean age was 57.7 years. The PROMIS 29 average cumulative T score was 42.9 with average change of −0.072 preoperatively versus postoperatively. Average sleep disturbance T score was 38.9 preoperatively and 41.4 postoperatively. There was no statistically significant difference in T score in any domain. The mean actigraphy activity data demonstrated near immediate return to baseline activity. Actigraphy sleep data demonstrate improvement in sleep fragmentation and decreased duration of awakenings.

Conclusions
Overall, patient-generated data detected differences in sleep and activity preoperatively versus postoperatively and demonstrated only a short period of activity disruption after CTR, which may be used when counseling patients. These data support actigraphy as a viable adjunct to traditional PROMS to evaluate the impact of surgical intervention and therefore may be useful in the study of other diseases affecting the upper extremity.
Prevention of Oxygen Desaturation in Morbidly Obese Patients During Electroconvulsive Therapy
Authors: Koyama Yukihide , Tsuzaki Koichi , Suzuki Takeshi , Ozaki Makoto , Saito Shigeru 
Published: February 2020

Abstract
In general, preoxygenation is performed using a face mask with oxygen in a supine position, and oxygenation is maintained with manual mask ventilation during electroconvulsive therapy (ECT). However, hypoxic episodes during ECT are not uncommon with this conventional method, especially in morbidly obese patients. The most important property of ventilatory mechanics in patients with obesity is reduced functional residual capacity (FRC). Thus, increasing FRC and oxygen reserves is an important step to improve oxygenation and prevent oxygen desaturation in these individuals. Head-up position, use of apneic oxygenation, noninvasive positive pressure ventilation, and high-flow nasal cannula help increase FRC and oxygen reserves, resulting in improved oxygenation and prolonged safe apnea period. Furthermore, significantly higher incidence of difficult mask ventilation is common in morbidly obese individuals. Supraglottic airway devices establish effective ventilation in patients with difficult airways. Thus, the use of supraglottic airway devices is strongly recommended in these patients. Conversely, because muscle fasciculation induced by depolarizing neuromuscular blocking agents markedly increases oxygen consumption, especially in individuals with obesity, the use of nondepolarizing neuromuscular blocking agents may contribute to better oxygenation in morbidly obese patients during ECT.
Halomonas urmiana sp. nov., a moderately halophilic bacterium isolated from Urmia Lake in Iran
Authors: Khan Shehzad Abid , Zununi Vahed Sepideh , Forouhandeh Haleh , Tarhriz Vahideh , Chaparzadeh Nader , Hejazi Mohammad Amin , Jeon Che Ok , Hejazi Mohammad Saeid 
Published: February 2020

In the course of screening halophilic bacteria in Urmia Lake in Iran, which is being threatened by dryness, a novel Gram-negative, moderately halophilic, heterotrophic and short rod-shaped bacteria was isolated and characterized. The bacterium was isolated from a water specimen and designated as TBZ3T. Colonies were found to be creamy yellow, with catalase- and oxidase-positive activities. The growth of strain TBZ3T was observed to be at 10–45 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 0.5–20 % (w/v) NaCl (optimum, 7.5 %). Strain TBZ3T contained C16 : 0, cyclo-C19 : 0
ω8c, summed feature 3 (comprising C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 8 (comprising C18 : 1
ω7c and/or C18 : 1
ω6c) as major fatty acids and ubiquinone-9 as the only respiratory isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid, unidentified phospholipid and unidentified polar lipids were detected as the major polar lipids. Strain TBZ3T was found to be most closely related to

Halomonas saccharevitans

AJ275T
, Halomonas denitrificans M29T and

Halomonas sediminicola

CPS11T with the 16S rRNA gene sequence similarities of 98.93, 98.15 and 97.60 % respectively and in phylogenetic analysis strain TBZ3T grouped with

Halomonas saccharevitans

AJ275T contained within a large cluster within the genus

Halomonas

. Based on phenotypic, chemotaxonomic and molecular properties, strain TBZ3T represents a novel species of the

Halomonas

genus, for which the name Halomonas urmiana sp. nov. is proposed. The type strain is TBZ3T (=DSM 22871T=LMG 25416T).
High precisionNeisseria gonorrhoeaevariant and antimicrobial resistance calling from metagenomic Nanopore sequencing
Authors: Sanderson Nicholas D , Swann Jeremy , Barker Leanne , Kavanagh James , Hoosdally Sarah , Crook Derrick ,   the GonFast Investigators Group, Street Teresa L , Eyre David W 
Published: February 2020

AbstractThe rise of antimicrobial resistantNeisseria gonorrhoeaeis a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhoea can recover near-completeN. gonorrhoeaegenomes. However, disentangling theN. gonorrhoeaegenome from metagenomic samples and robustly identifying antimicrobial resistance determinants from error-prone Nanopore sequencing is a substantial bioinformatics challenge.Here we demonstrate anN. gonorrhoeaediagnostic workflow for analysis of metagenomic sequencing data obtained from clinical samples using R9.4.1 Nanopore sequencing. We compared results from simulated and clinical infections with data from known reference strains and Illumina sequencing of isolates cultured from the same patients. We evaluated three Nanopore variant callers and developed a random forest classifier to filter called SNPs. Clair was the most suitable variant caller after SNP filtering. A minimum depth of 20x reads was required to confidently identify resistant determinants over the entire genome. Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic information inN. gonorrhoeaeinfection.
Improving model-based fNIRS analysis using mesh-based anatomical and light-transport models
Authors: Tran Anh Phong , Yan Shijie , Fang Qianqian 
Published: February 2020

AbstractSignificanceFunctional near-infrared spectroscopy (fNIRS) has become an important research tool in studying human brains. Accurate quantification of brain activities via fNIRS relies upon solving computational models that simulate the transport of photons through complex anatomy.AimWe aim to highlight the importance of accurate anatomical modeling in the context of fNIRS, and propose a robust method for creating high-quality brain/full-head tetrahedral mesh models for neuroimaging analysis.ApproachWe have developed a surface-based brain meshing pipeline that can produce significantly better brain mesh models compared to conventional meshing techniques. It can convert segmented volumetric brain scans into multi-layered surfaces and tetrahedral mesh models, with typical processing times of only a few minutes and broad utilities, such as in Monte Carlo or finite-element based photon simulations for fNIRS studies.ResultsA variety of high quality brain mesh models have been successfully generated by processing publicly available brain atlases. In addition, we compare 3 brain anatomical models - the voxel-based brain segmentation, tetrahedral brain mesh and layered-slab brain model, and demonstrate noticeable discrepancies in brain partial-pathlengths when using approximated brain anatomies, ranging between −1.5-23% with the voxelated brain and 36-166% with the layered-slab brain.ConclusionThe generation and utility of high-quality brain meshes can lead to more accurate brain quantification in fNIRS studies. Our open-source meshing toolboxes “Brain2Mesh” and “Iso2Mesh” are freely available at http://mcx.space/brain2mesh.
Rescue Ebola Patients in silico
Authors: Zhao Gang , Binder Sebastian , Pongratz Georg , Meyer-Hermann Michael 
Published: February 2020

AbstractEbola, one of the most pathogenic and lethal viruses, repeatedly leads to severe outbreaks with large numbers of casualties. By integration of data of fatal, non-fatal and asymptomatic cases, we developed a mathematical model of the immune response to Ebola infections and found that TNF-α can explain subsequent cytokine responses and allows to quantitatively stratify patients into survivors and fatal cases. The model further suggests that antibodies provide the key resolving mechanism in survivors while IFN-γ is the key defense mechanism in fatal cases. Exogenous IFN-γ and inhibition of excessive inflammation have the potential to rescue fatal Ebola infections in silico. In view of the high mortality of this disease, limited real life studies, and the unforeseeable next outbreak, our in silico analysis is meant as a guide for future research by the determination of the most efficient strategies for Ebola treatment.
Binding affinity and conformational preferences influence kinetic stability of short oligonucleotides on carbon nanotubes
Authors: Alizadehmojarad Ali A. , Zhou Xingcheng , Beyene Abraham G. , Chacon Kevin , Sung Younghun , Landry Markita P. , Vuković Lela 
Published: February 2020

AbstractDNA-wrapped single walled carbon nanotubes (SWNTs) have found a widespread use in a variety of nanotechnology applications. Yet, the relationship between structural conformation, binding affinity and kinetic stability of these polymers on SWNTs remains poorly understood. Here, we used molecular dynamics (MD) simulations and experiments to explore this relationship for short oligonucleotides adsorbed on SWNTs. First, using classical MD simulations of oligonucleotide-(9,4)-SWNT hybrid complexes, we explored the relationship between ssDNA and ssRNA surface conformation and sequence chemistry. We screened the conformation of 36 sequences of short ssDNA and ssRNA polymers on (9,4) SWNT, where the contour lengths were selected so the polymers can, to a first approximation, wrap once around the SWNT circumference. From these screens, we identified structural motifs that we broadly classified into “rings” and “non-rings.” Then, several sequences were selected for detailed investigations. We used temperature replica exchange MD calculations to compute two-dimensional free energy landscapes characterizing the conformations of select sequences. “Ring” conformations seemed to be driven primarily by sequence chemistry. Specifically, strong (n,n+2) nucleotide interactions and the ability of the polymer to form compact structures, as for example, through sharp bends in the nucleotide backbone, correlated with ring-forming propensity. However, ring-formation probability was found to be uncorrelated with free energy of oligonucleotide binding to SWNTs (ΔGbind). Conformational analyses of oligonucleotides, computed free energy of binding of oligonucleotides to SWNTs, and experimentally determined kinetic stability measurements show that ΔGbindis the primary correlate for kinetic stability. The probability of the sequence to adopt a compact, ring-like conformation is shown to play a secondary role that still contributes measurably to kinetic stability. For example, sequences that form stable compact rings (C-rich sequences) could compensate for their relatively lower ΔGbindand exhibit kinetic stability, while sequences with strong ΔGbind(such as (TG)3(GT)3) were found to be kinetically stable despite their low ring formation propensity. We conclude that the stability of adsorbed oligonucleotides is primarily driven by its free energy of binding and that if ring-like structural motifs form, they would contribute positively to stability.Abstract Figure
Valorization of CO2through lithoautotrophic production of sustainable chemicals inCupriavidus necator
Authors: Nangle Shannon N. , Ziesack Marika , Buckley Sarabeth , Trivedi Disha , Loh Daniel M. , Nocera Daniel G. , Silver Pamela A. 
Published: February 2020

AbstractCoupling recent advancements in genetic engineering of diverse microbes and gas-driven fermentation provides a path towards sustainable commodity chemical production.Cupriavidus necatorH16 is a suitable species for this task because it effectively utilizes H2and CO2and is genetically tractable. Here, we demonstrate the versatility ofC. necatorfor chemical production by engineering it to produce three products from CO2under lithotrophic conditions: sucrose, polyhydroxyalkanoates (PHAs), and lipochitooligosaccharides (LCOs). We engineered sucrose production in a co-culture system with heterotrophic growth 30 times that of WTC. necator. We engineered PHA production (20-60% DCW) and selectively altered product composition by combining different thioesterases and phaCs to produce copolymers directly from CO2. And, we engineeredC. necatorto convert CO2into the LCO, a plant growth enhancer, with titers of ∼1.4 mg/L—equivalent to yields in its native source,Bradyrhizobium. We applied the LCOs to germinating seeds as well as corn plants and observed increases in a variety of growth parameters. Taken together, these results expand our understanding f how a gas-utilizing bacteria can promote sustainable production.
Deep Neural Networks Point to Mid-level Complexity of Rodent Object Vision
Authors: Vinken Kasper , de Beeck Hans Op 
Published: February 2020

AbstractIn the last two decades rodents have been on the rise as a dominant model for visual neuroscience. This is particularly true for earlier levels of information processing, but high-profile papers have suggested that also higher levels of processing such as invariant object recognition occur in rodents. Here we provide a quantitative and comprehensive assessment of this claim by comparing a wide range of rodent behavioral and neural data with convolutional deep neural networks. These networks have been shown to capture the richness of information processing in primates through a succession of convolutional and fully connected layers. We find that rodent object vision can be captured using low to mid-level convolutional layers only, without any convincing evidence for the need of higher layers known to simulate complex object recognition in primates. Our approach also reveals surprising insights on assumptions made before, for example, that the best performing animals would be the ones using the most complex representations – which we show to likely be incorrect. Our findings suggest a road ahead for further studies aiming at quantifying and establishing the richness of representations underlying information processing in animal models at large.
Evaluation of excavation-induced movements through case histories in Hangzhou
Authors: Ying Hong-Wei , Cheng Kang , Zhang Li-Sha , Ou Chang-Yu , Yang Yong-Wen 
Published: February 2020

Purpose
Deep excavation in soft clay often causes additional deformations to surroundings. Then, if deformations cannot be predicted reasonably, the adjacent buildings may be threatened by the deep excavation. Based on the good field observations from ten deep excavations in Hangzhou, this paper aims to thoroughly investigate the characteristics of wall deflections and ground settlements induced by deep excavations.

Design/methodology/approach
On the basis of good field observation of ten deep excavations, the performances of excavations, supported by contiguous pile in Hangzhou, were studied, and also compared with other case histories.

Findings
The maximum wall deflections (dhm) rang mostly from 0.7 to 1.2 per cent He, where He is the final excavation depth, larger than those in Taipei and Shanghai. The observed maximum ground settlement in the Hangzhou cases generally ranges from 0.2 to 0.8 per cent He. Then, the settlement influence zone extends to a distance of 2.0-4.0 He from the excavation. The relatively large movements and influence zones in Hangzhou may be attributed to low stability numbers, large excavation widths and the creep effect. The excavation width is justified to have a significant influence on the wall deflection. Therefore, to establish a semi-empirical formula for predicting the maximum wall deflection, it is necessary to include the factor of excavation width.

Originality/value
The relevant literature concentrated on the characteristics of deep excavations supported by the contiguous pile wall in Hangzhou soft clay can rarely be found. Based on the ten deep excavations with good field observation in Hangzhou, the characteristics of wall deflection and ground settlements were comprehensively studied for the first time, which can provide some theoretical support for similar projects.
A counterexample to FORM and SORM
Authors: Ávila da Silva Júnior Claudio Roberto , Damazio Pedro Danizete , Matioli Luiz Carlos , Cavichiolo João Lucas 
Published: February 2020

PurposeThis paper aims to presents a counterexample that points to an inconsistency generated by the first- and second-order approximation methods, FORM and SORM, respectively, procedures for elliptical problems.Design/methodology/approachThe classical results of theory measure and functional analysis were used.FindingsThe FORM and SORM are known to find solutions in a Gaussian space. This procedure does not satisfy the conditions of the Lax–Milgram theorem and does not assure the existence and uniqueness of the solution.Research limitations/implicationsThis paper alerts the engineering research community that uses these methods, initiating discussion and improvement of FORM and SORM procedures.Practical implicationsThis paper puts in check the feasibility of using FORM and SORM in engineering problems.Originality/valueFrom the moment they were introduced to the engineering and scientific communities, the FORM and SORM were taken as the bases for solving various problems found in the literature and indifferent documents scattered throughout the world over the past 50 years, for FORM, and 40 years, for SORM. Even though it was a very serious fault, at least for elliptical problems, pointed out in this work, it went unnoticed all those years by the research community. Therefore, the contribution of this paper is to present the engineering community that uses FORM and SORM in elliptical problems an unnoticed failure since the introduction of these methods.
Contractor prequalification for green buildings—evidence from Turkey
Authors: Gurgun Asli Pelin , Koc Kerim 
Published: February 2020

PurposeCompetent contractors are one of the critical stakeholders to achieve targeted sustainability objectives in green building (GB) projects. Prior to contractor selection, prequalification is an important step, which requires contractors with certain capabilities in addition to traditional features. This study aims to develop a systematic and practical model for prequalification in GB projects using a multi-criteria decision-making (MCDM) approach by adopting the analytical hierarchy process (AHP).Design/methodology/approachTheAHP model with 8 main criteria groups and 25 sub-criteria is structured based on literature review and professional opinions accompanied by a pilot study. Then, interviews with experts, who are experienced in the development and application phases of GB projects in Turkey, are arranged to collect judgements. The agreement levels between different groups of experts are analysed via Pearson's and Spearman's rank correlation coefficient. Model applicability is tested on six hypothetical contractors for practicality.FindingsThe results show that i) financial capabilities, ii) legal status and iii) sustainability groups are the top three main criteria, while i) compliance with schedule requirements of the client, ii) current legal status including suits, iii) negative litigation history records, iv) contractor's compliance capacity to client's sustainability checklist for the proposed project and v) sustainability with lower life cycle cost (durability, maintenance, constructability) are the top five sub-criteria.Originality/valueThere is a gap in the literature analysing contractor prequalification phase in GB projects. This study attempts to fill this lack provided with a practical evaluation tool.