bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes in Temporary ICUs Versus Conventional ICUs: An Observational Cohort of Mechanically Ventilated Patients With COVID-19–Induced Acute Respiratory Distress Syndrome
Authors: Jimenez Jose Victor , Olivas-Martinez Antonio , Rios-Olais Fausto Alfredo , Ayala-Aguillón Frida , Gil- López Fernando , Leal-Villarreal Mario Andrés de Jesús , Rodríguez-Crespo Juan José , Jasso-Molina Juan C. , Enamorado-Cerna Linda , Dardón-Fierro Francisco Eduardo , Martínez-Guerra Bernardo A. , Román-Montes Carla Marina , Alvarado-Avila Pedro E. , Juárez-Meneses Noé Alonso , Morales-Paredes Luis Alberto , Chávez-Suárez Adriana , Gutierrez-Espinoza Irving Rene , Najera-Ortíz María Paula , Martínez-Becerril Marina , Gonzalez-Lara María Fernanda , Ponce de León-Garduño Alfredo , Baltazar-Torres José Ángel , Rivero-Sigarroa Eduardo , Dominguez-Cherit Guillermo , Hyzy Robert C. , Kershenobich David , Sifuentes-Osornio José 
Published: March 2022

IMPORTANCE:
Throughout the COVID-19 pandemic, thousands of temporary ICUs have been established worldwide. The outcomes and management of mechanically ventilated patients in these areas remain unknown.

OBJECTIVES:
To investigate mortality and management of mechanically ventilated patients in temporary ICUs.

DESIGN, SETTING, AND PARTICIPANTS:
Observational cohort study in a single-institution academic center. We included all adult patients with severe COVID-19 hospitalized in temporary and conventional ICUs for invasive mechanical ventilation due to acute respiratory distress syndrome from March 23, 2020, to April 5, 2021.

MAIN OUTCOMES AND MEASURES:
To determine if management in temporary ICUs increased 30-day in-hospital mortality compared with conventional ICUs. Ventilator-free days, ICU-free days (both at 28 d), hospital length of stay, and ICU readmission were also assessed.

RESULTS:
We included 776 patients (326 conventional and 450 temporary ICUs). Thirty-day in-hospital unadjusted mortality (28.8% conventional vs 36.0% temporary, log-rank test p = 0.023) was higher in temporary ICUs. After controlling for potential confounders, hospitalization in temporary ICUs was an independent risk factor associated with mortality (hazard ratio, 1.4; CI, 1.06–1.83; p = 0.016).There were no differences in ICU-free days at 28 days (6; IQR, 0–16 vs 2; IQR, 0–15; p = 0.5) or ventilator-free days at 28 days (8; IQR, 0–16 vs 5; IQR, 0–15; p = 0.6). We observed higher reintubation (18% vs 12%; p = 0.029) and readmission (5% vs 1.6%; p = 0.004) rates in conventional ICUs despite higher use of postextubation noninvasive mechanical ventilation (13% vs 8%; p = 0.025). Use of lung-protective ventilation (87% vs 85%; p = 0.5), prone positioning (76% vs 79%; p = 0.4), neuromuscular blockade (96% vs 98%; p = 0.4), and COVID-19 pharmacologic treatment was similar.

CONCLUSIONS AND RELEVANCE:
We observed a higher 30-day in-hospital mortality in temporary ICUs. Although both areas had high adherence to evidence-based management, hospitalization in temporary ICUs was an independent risk factor associated with mortality.
Efficacy of Combined Hiatal Hernia Repair and Transoral Incisionless Fundoplication for Giant Paraoesophageal Hernias: Technique and Early Results
Authors: Gergen Anna K. , Wagh Mihir S. , Menard-Katcher Paul , Pratap Akshay 
Published: March 2022

Introduction:
Data is limited on hybrid transoral incisionless fundoplication (TIF) and hiatal hernia repair in giant paraoesophageal hernia (GPEH). We aimed to assess the safety, patient satisfaction, and symptom resolution following a hybrid paraoesophageal hernia (PEH) repair and TIF in patients with GPEH.

Patients and Methods:
All single-session hybrid TIF combined with minimally invasive PEH repair performed between February 2020 and June 2021 were evaluated. Procedures were performed in the operating room under general anesthesia with robotic or laparoscopic PEH repair followed by TIF.

Results:
Twelve patients underwent combined surgical hiatal hernia repair and TIF. Primary presenting symptoms included heartburn (75.0%), dysphagia (41.7%), and chronic anemia from Cameron’s ulcers (16.7%). The mean hernia defect size was 5.0 cm (range 3.0 to 6.0 cm). Hiatal hernia repairs were performed robotically in 7 patients and laparoscopically in 5 patients. The total mean operative time was 254 minutes (range: 180 to 390 min). One patient reported postoperative dysphagia requiring endoscopic dilation postdischarge with a resolution of symptoms. No gas-bloat symptoms were reported. All patients reported complete resolution of presenting symptoms at the time of follow-up. Postoperative mean follow-up for 4 patients at 6 months with upper endoscopy and pH testing showed an intact valve with no evidence of esophagitis or acid reflux.

Conclusions:
In our experience, hybrid hiatal hernia repair and TIF is a safe and effective therapeutic option for patients with GPEH. This hybrid procedure allows for more expeditious completion of the repair and results in lower rates of postfundoplication dysphagia and gas-bloat. Furthermore, this approach requires a less extensive surgical dissection on the greater curvature of the stomach, thereby minimizing the risk of vagal nerve injury and bleeding from the short gastric vessels.
How Should Acute T-cell Mediated Rejection of Kidney Transplants Be Treated: Importance of Follow-up Biopsy
Authors: Aziz Fahad , Parajuli Sandesh , Garg Neetika , Mohamed Maha , Zhong Weixiong , Djamali Arjang , Mandelbrot Didier 
Published: March 2022

Background.
Limited published data exist to guide patient monitoring after the treatment of T-cell mediated rejection (TCMR) of kidney allografts.

Methods.
We reviewed the kidney function and histological outcomes after treatment of 163 first episodes of biopsy-proven TCMR between January 1‚ 2015‚ and July 31‚ 2020.

Results.
Of the 146 patients treated with steroid pulse alone, complete histological response was seen in 83% of patients with borderline rejection, 82.5% with grade 1A, 67% with grade 1B, and 50% with grade IIA. Of the 17 patients treated with steroids plus antithymocyte globulin, the complete histological response rate was 100% with grade 1A, 75% with grade 1B, 100% with grade IIA, and 57% with grade IIB. Among the patients with complete response as assessed by kidney function, 14% only had a partial or no response histologically. Among patients with no kidney function response, 68% had a complete response histologically.

Conclusion.
We thus find that responses based on kidney function alone do not correlate well with histological responses. If further treatment had been based solely on changes in estimated glomerular filtration rate, a significant number of patients would have been subsequently undertreated or overtreated. These results support the use of protocol follow-up biopsies after the treatment of TCMR.
Clinical Validation of a Plasma Donor-derived Cell-free DNA Assay to Detect Allograft Rejection and Injury in Lung Transplant
Authors: Rosenheck Justin P. , Ross David J. , Botros Mena , Wong Alexander , Sternberg Jonathan , Chen Yen-An , Liang Nathan , Baer Amy , Ahmed Ebad , Swenerton Ryan , Zimmermann Bernhard G. , Fehringer Gordon , Demko Zachary P. , Olymbios Michael , Billings Paul R. , Keller Brian C. 
Published: March 2022

Background.
Lung transplant patients are vulnerable to various forms of allograft injury, whether from acute rejection (AR) (encompassing acute cellular rejection [ACR] and antibody-mediated rejection [AMR]), chronic lung allograft dysfunction (CLAD), or infection (INFXN). Previous research indicates that donor-derived cell-free DNA (dd-cfDNA) is a promising noninvasive biomarker for the detection of AR and allograft injury. Our aim was to validate a clinical plasma dd-cfDNA assay for detection of AR and other allograft injury and to confirm and expand on dd-cfDNA and allograft injury associations observed in previous studies.

Methods.
We measured dd-cfDNA fraction using a novel single-nucleotide polymorphism-based assay in prospectively collected plasma samples paired with clinical-pathologic diagnoses. dd-cfDNA fraction was compared across clinical-pathologic cohorts: stable, ACR, AMR, isolated lymphocytic bronchiolitis, CLAD/neutrophilic-responsive allograft dysfunction (NRAD), and INFXN. Performance characteristics were calculated for AR and combined allograft injury (AR + CLAD/NRAD + INFXN) versus the stable cohort.

Results.
The study included 195 samples from 103 patients. Median dd-cfDNA fraction was significantly higher for ACR (1.43%, interquartile range [IQR]: 0.67%–2.32%, P = 5 × 10−6), AMR (2.50%, IQR: 2.06%–3.79%, P = 2 × 10−5), INFXN (0.74%, IQR: 0.46%–1.38%, P = 0.02), and CLAD/NRAD (1.60%, IQR: 0.57%–2.60%, P = 1.4 × 10−4) versus the stable cohort. Area under the receiver operator characteristic curve for AR versus stable was 0.91 (95% confidence interval [CI]: 0.83-0.98). Using a ≥1% dd-cfDNA fraction threshold, sensitivity for AR was 89.1% (95% CI: 76.2%-100.0%), specificity 82.9% (95% CI: 73.3%-92.4%), positive predictive value, 51.9% (95% CI: 37.5%-66.3%), and negative predictive value, 97.3% (95% CI: 94.3%-100%). For combined allograft injury area under the receiver operator characteristic curve was 0.76 (95% CI: 0.66-0.85), sensitivity 59.9% (95% CI: 46.0%-73.9%), specificity 83.9% (95% CI: 74.1%-93.7%), positive predictive value, 43.6% (95% CI: 27.6%-59.6%), and negative predictive value, 91.0% (95% CI: 87.9%-94.0%).

Conclusions.
These results indicate that our dd-cfDNA assay detects AR and other allograft injury. dd-cfDNA monitoring, accompanied by standard clinical assessments, represents a valuable precision tool to support lung transplant health and is appropriate for further assessment in a prospective randomized-controlled study.
Quantum flux densities for electronic–nuclear motion: exact versus Born–Oppenheimer dynamics
Authors: Schaupp Thomas , Engel Volker 
Published: March 2022

We study the coupled electronic–nuclear dynamics in a model system to compare numerically exact calculations of electronic and nuclear flux densities with those obtained from the Born–Oppenheimer (BO) approximation. Within the adiabatic expansion of the total wave function, we identify the terms which contribute to the flux densities. It is found that only off-diagonal elements that involve the interaction between different electronic states contribute to the electronic flux whereas in the nuclear case the major contribution belongs to the BO electronic state. New flux densities are introduced where in both, the electronic and the nuclear case, the main contribution is contained in the component corresponding to the BO state. As a consequence, they can be determined within the BO approximation, and an excellent agreement with the exact results is found.
This article is part of the theme issue ‘Chemistry without the Born–Oppenheimer approximation’.
Mixed-quantum-classical or fully-quantized dynamics? A unified code to compare methods
Authors: Coonjobeeharry J. , Spinlove K. E. , Sanz Sanz C. , Sapunar M. , Došlić N. , Worth G. A. 
Published: March 2022

Three methods for non-adiabatic dynamics are compared to highlight their capabilities. Multi-configurational time-dependent Hartree is a full grid-based solution to the time-dependent Schrödinger equation, variational multi-configurational Gaussian (vMCG) uses a less flexible but unrestricted Gaussian wavepacket basis, and trajectory surface hopping (TSH) replaces the nuclear wavepacket with a swarm of classical trajectories. Calculations with all methods using a model Hamiltonian were performed. The vMCG and TSH were also then run in adirect dynamicsmode, with the potential energy surfaces calculated on-the-fly using quantum chemistry calculations. All dynamics calculations used the Quanticspackage, with the TSH calculations using a new interface to a surface hopping code. A novel approach to calculate adiabatic populations from grid-based quantum dynamics using a time-dependent discrete variable representation is presented, allowing a proper comparison of methods.This article is part of the theme issue ‘Chemistry without the Born–Oppenheimer approximation’.
Key residue on cytoplasmic dynein for asymmetric unbinding and unidirectional movement along microtubule
Authors: Kubo Shintaroh , Shima Tomohiro , Kon Takahide , Takada Shoji 
Published: March 2022

AbstractCytoplasmic dynein 1 is almost exclusively responsible for intracellular transport toward the minus-end of microtubules in animal cells. One of the key factors for the unidirectional movement of dynein is the asymmetry of the unbinding of the motor from the microtubule when an external load is applied; it dissociates more easily from microtubules with minus-end directed loading than with plus-end directed loading. To elucidate the molecular basis for this property, we performed molecular dynamics simulations to identify the key residues responsible for asymmetry, which were then examined experimentally. First, we reproduced asymmetry in the unbinding behavior of dynein using coarse-grained simulations. Then, data analysis together with mutational analysis in silico predicted the specific residues that may be responsible for the asymmetry in unbinding. To examine this prediction, we expressed and purified recombinant dynein with mutations in either of the identified key residues. Consistent with the simulations, one of the mutants did not exhibit asymmetry in the in vitro unbinding assay. Moreover, the mutant dynein was able to bind and move diffusely along a microtubule but was unable to restrict its movement to the minus-end direction. Our results demonstrate both experimentally and theoretically how the key residue on the microtubule-binding domain generates asymmetry in unbinding, which is a critical mechanism for the unidirectional movement of dynein along a microtubule track.Significance StatementCytoplasmic dynein moves to the minus end of microtubules. This unidirectional dynein motility provides the driving force for various cellular activities including vesicle transport, organelle positioning and cell division. One of the key factors for dynein to exhibit unidirectional movement is the asymmetry of unbinding of dynein from the microtubule depending on the direction of external load. By combining computational simulations and in vitro experiments, we identified a residue responsible for the asymmetry. A point mutation at the residue indeed abolished unidirectional motility, highlighting the importance of the asymmetric unbinding property in dynein’s unidirectional movement.
SCExecute: cell barcode-stratified analyses of scRNA-seq data
Authors: Edwards Nathan , Dillard Christian , Prashant NM , Liu Hongyu , Yang Mia , Ulianova Evgenia , Horvath Anelia 
Published: March 2022

AbstractMotivationIn single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are not supported by available tools that are designed for bulk RNA-Seq data.ResultsWe introduce a tool – SCExecute – which executes a user-provided command on barcode-stratified, extracted on-the-fly, single cell binary alignment map (scBAM) files. SCExecute extracts the cell barcode from aligned, pooled single-cell sequencing data. The user-specified command option executes all the commands defined in the session from monolithic programs and multi-command shell-scripts to complex shell-based pipelines. The execution can be further restricted to barcodes or/and genomic regions of interest. We demonstrate SCExecute with two popular variant callers - GATK and Strelka2 – combined with modules for bam file manipulation and variant filtering, to detect single cell-specific expressed Single Nucleotide Variants (sceSNVs) from droplet scRNA-seq data (10X Genomics Chromium System).ConclusionSCExecute facilitates custom cell-level analyses on barcoded scRNA-seq data using currently available tools and provides an effective solution for studying low (cellular) frequency transcriptome features.AvailabilitySCExecute is implemented in Python3 using the PySAM package and distributed for Linux and Python environments from https://github.com/HorvathLab/NGS/tree/master/SCExecute.
Osmotic stress via calmodulin lead to the formation of stress granule in Drosophila S2 cells
Authors: Zhang Chujun , Grond Rianne , Damen J. Mirjam A. , Wu Wei , Rabouille Catherine 
Published: March 2022

AbstractCellular stress of S2 cells leads to the formation of stress assemblies by phase separation of cytoplasmic components. We have shown that the cellular stresses of either high increase of the NaCl concentration in the extracellular medium, or a moderate one combined to amino acid starvation, leads to the formation of Sec bodies where components of the endoplasmic Reticulum exit sites (ERES) coalesce. These extracellular stresses lead to both the activation of salt inducible kinase (SIK), and to ER stress triggering the activation of the two downstream kinases IRE1 and PERK. Interestingly, the same stresses also result in the formation of a second stress assembly, the stress granules, which stores specific RNAs and RNA binding proteins. Here we asked whether stress granule formation is governed by the same pathways as Sec bodies. However, we found that the inhibition of SIK, IRE1 and PERK does not affect stress granule formation. Instead, we found that osmotic stress through the addition of either salts (including calcium chloride) or sucrose leads to the formation of stress granules. Interestingly, stress granule formation is partly modulated by calmodulin activation, suggesting the involvement of calcium signaling. Furthermore, as Sec body formation is driven by entirely different pathways, these results show that the same cells under the same stress, form two different stress assemblies by non-overlapping downstream pathway activation, perhaps explaining that they do not coalescence into a single structure.
A fraction of an executive: new ways to save and compete
Authors: So Maggie , Teckchandani Atul 
Published: March 2022

Purpose
A new way for business leaders to access targeted professional help is via fractional service providers. Fractional service providers can provide tremendous advantages, as they are much more closely associated with the company than outsourcing or consulting service providers, while being more cost effective than full-time employees. A fractional service provider that can be of particular benefit to startups and small businesses is a fractional CFO or Controller – who can provide an organization with the skills to perform all of the activities that a finance and accounting department should perform and provide a consistent leadership voice on all finance-related matters.

Design/methodology/approach
This paper first introduces fractional services and discusses how fractional service providers differ from outsourcing, consulting engagements and full-time employment. Then, it presents an explanation of why fractional service providers may be best suited to manage the finance and accounting functions in a small or medium-sized business. Finally, it discusses factors that business leaders should consider and best practices they should use when using fractional services.

Findings
Using a fractional CFO or Controller will provide an increased focus on the company’s financial health and allow the organization to perform (or oversee) all of the activities that a finance and accounting department should be performing. The scope of work a fractional CFO or Controller performs can be easily modified to meet the needs of the firm, Moreover, they require little direct management. As a result, a fractional CFO or Controller can often be a more cost-effective option than hiring for the finance and accounting function on a full-time basis.

Originality/value
In today’s world, organizations are increasingly seeking ways to maintain effectiveness while also being flexible in how human capital is used. This paper discusses one such flexibility: incorporating fractional service providers. The key premise of this paper is that fractional service providers, specifically fractional CFOs or Controllers, can be an extremely effective way for many organizations, especially small businesses and startups, to get more sophisticated help and guidance in finance and accounting-related matters – thereby acting as an excellent bridge between an ineffective finance and accounting function and creating such a function staffed by full-time employees.
Competing with artificial intelligence – can the records and information management profession withstand the challenge?
Authors: Xie Sherry Li , Siyi Li , Han Ruohua 
Published: March 2022

PurposeTo report on a study that focused on the records and information management (RIM) profession’s competencies with respect to the development of AI.Design/methodology/approachDesigned as deductive, the study distilled artificial intelligence (AI) insusceptibility indicators, creative intelligence and social intelligence, from the Oxford study and applied them to the current RIM core competencies developed by ARMA International. Manual coding and semantic analysis served as the primary inquiring methods, and both statistical and qualitative results are presented.FindingsThe RIM profession as a whole is currently AI-resistant, yet it is not AI-proof. To be AI-proof, the existent competencies model needs to be redesigned as the AI-resistant parts are mingled with AI-prone ones, and the prescriptions of some RIM theories and principles are not ready for AI judgements or adjustments. It requires also strategizing collaborations among all stakeholders so that we can be one step ahead of future unfavorable organizational decisions. If our professional nature renders us AI-resistant for now, then it is our professional unity that will ensure us AI-proof in the future.Originality/valueTo the best of the authors’ knowledge, this paper is first of its kind within the international RIM community. It provides detailed assessment data on AI insusceptibility and targeted suggestions regarding the RIM community as a whole.
Rethinking the M&A process: Learning private equity’s secret to outperforming corporate strategic acquirers
Authors: Gilligan John , Galpin Timothy 
Published: March 2022

Purpose
Although M&A transactions often destroy shareholder value for corporate strategic buyers, PE firms, whose business model is predicated upon repeating M&A, have a better record of creating value for their investors.

Design/methodology/approach
The critical aspects that comprise the PE playbook are organized around the three main deal phases Pre-deal, Deal and Post-deal.

Findings
Research has found that 60 percent of surveyed strategic buyer executives indicated their companies do not have a comprehensive end-to-end M&A approach using a playbook.

Practical/implications
Ample evidence exists demonstrating that corporate strategic buyers experience significant difficulty in creating value from their transactions.

Originality/value
Though many view PE firms as value-destroyers, various peer-reviewed studies have found that PE-backed firms have a surprisingly favorable record.