bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleation Parameters of SPC/E And TIP4P/2005 Water Vapor Measured In NPT Molecular Dynamics Simulations
Authors: Němec Tomáš 
Published: January 2022

Abstract
Nucleation rates for droplet formation in water vapor are measured in molecular dynamics simulations of SPC/E and TIP4P/2005 water by monitoring individual nucleation events. The nucleation process is simulated in the NPT ensemble to evaluate the steady-state nucleation rate in accordance with the assumptions of classical nucleation theory (CNT). Nucleation rates measured between 300 K and 425 K for the SPC/E model, and between 325 K and 475 K for the TIP4P/2005 model, agree with the CNT predictions roughly within the standard deviation of the MD measurements of the nucleation rates.
Towards Modelling of Evacuation Behavior and Planning for Emergency Logistics Due to the Philippine Taal Volcanic Eruption in 2020
Authors: Lim Hector , Lim Ma. Bernadeth , Rojas Ann Wendy 
Published: January 2022

Abstract
Emergency evacuation is the immediate escape of people away from a place of an imminent threat to a place of safety. The ability of the households to evacuate is a crucial component in reducing disaster risk. Logistical issues such as a lack of resources during and after the evacuation, as well as road congestion, might arise, especially in short and no-notice calamities such as a volcanic eruption. This study examines the relationship of variables of evacuation logistics of Barangay Banga, Talisay, Batangas in the context of the 2020 Taal Volcanic eruption. A survey was conducted based on the experience of the households during the volcanic eruption. A descriptive statistical analysis was performed for all the variables on household evacuation logistics to understand the behavior of households as they make decisions during emergencies. These variables include the type of evacuation, departure timing, evacuation mode choice, and destination choice. Additionally, a pairwise correlation was employed to identify the influential factors related to household evacuation logistics such as socio-demographic and household characteristics, hazard-related factors as well as their experience with Taal Volcano’s recurring activities. The results of this study aim to provide insights to a better understanding of the evacuation behavior of households in the context of a volcanic eruption and be useful in the evacuation logistics planning of the country.
Comparison Between Culture-Positive and Culture-Negative Septic Shock in Emergency Department Patients
Authors: Huang Yen-Chang , Hung Chi-Chieh , Yang Yong-Ye , Wang Tsung-Han , Hsu Yin-Chou 
Published: January 2022

Abstract
Culture results in patients with septic shock affect their management strategies. Our study aimed to compare the clinical characteristics and outcomes of patients with culture-negative septic shock (CNSS) and culture-positive septic shock (CPSS). A single-center, retrospective, case-control study included adult patients diagnosed with septic shock in the emergency department between January 1, 2019 and March 31, 2020. They were divided into CNSS and CPSS groups based on their culture results. Patients with CPSS (63.7%, 311/488) and CNSS (36.3%, 177/488) were identified. The CPSS and CNSS groups had comparable clinical outcomes, including mechanical ventilation (29.6% vs. 32.8%, p = 0.46), renal replacement therapy (19.3% vs. 23.2%, p = 0.31), intensive care unit care (51.8% vs. 45.2%, p = 0.16), 30-day (35.7% vs. 36.7%, p = 0.82) and in-hospital mortality (39.5% vs. 41.8%, p = 0.63). The duration (13 [8−19] vs. 16 [10−23], days, p = 0.04) and de-escalation timing (5 [2−10] vs. 9 [7−12], day, p = 0.02) of antibiotic administration in the CNSS group was significantly shorter and earlier than in the CPSS group. Patients with CNSS and CPSS had similar clinical characteristics and adverse outcome proportions. Physicians can evaluate the feasibility of early de-escalation or discontinuation of antibiotic administration in CNSS patients with clinical improvement.
Benzyl Farnesyl Amine Mimetics are Potent Inhibitors of the Sterol Biosynthesis Pathway in Leishmania Amazonensis Leading to Oxidative Stress, Growth Arrest, and Ultrastructural Alterations
Authors: Macedo-Silva Sara Teixeira , Visbal Gonzalo , Souza Gabrielle Frizzo , Santos Mayara Roncaglia dos , Cämmerer Simon B. , de Souza Wanderley , Rodrigues Juliany Cola Fernandes 
Published: January 2022

Abstract
Leishmaniasis is a neglected disease caused by protozoan parasites of the Leishmania genus spread around the world. Benzyl farnesyl amine mimetics are known class of compounds selectively designed to inhibit the squalene synthase (SQS) enzyme that catalyzes the first committed reaction on the sterol biosynthesis pathway. Herein, we studied seven new benzyl farnesyl amine mimetics (SBC 37 - 43) against Leishmania amazonensis. After the first initial screening of cell viability, two inhibitors (SBC 39 and SBC 40) were selected for further studies. Against intracellular amastigotes, SBC 39 and SBC 40 presented selectivity indexes of 117.7 and 180, respectively, indicating that they are highly selective. Analyses of free sterol showed that SBC 39 and SBC 40 inhibit two enzymes, sterol Δ8 → Δ7 isomerase and SQS, resulting in depletion of endogenous 24-methyl sterols. Physiological analysis and electron microscopy revealed three main alterations: 1) in the mitochondrion ultrastructure and function; 2) the presence of lipid bodies and autophagosomes; and 3) the appearance of projections in the plasma membrane and extracellular vesicles inside the flagellar pocket. In conclusion, our results support the notion that benzyl farnesyl amine mimics have a potent effect against Leishmania amazonensis and should be an interesting novel pharmaceutical lead for the development of new chemotherapeutic alternatives to treat leishmaniasis.
Linking Physical Activity to Personal Values: Feasibility and Acceptability Randomized Pilot of a Behavioral Intervention for Older Adults with Osteoarthritis Pain
Authors: Vilardaga Jennifer C Plumb , Kelleher Sarah , Diachina Allison , Riley Jennie , Somers Tamara 
Published: January 2022

Abstract
Background

Osteoarthritis (OA) pain is common and leads to functional impairment for many older adults. Physical activity can improve OA outcomes for older adults, but few are appropriately active. Behavioral interventions can reduce barriers to physical activity. We developed and tested a brief, novel behavioral intervention for older adults combining values to enhance motivation and strategic activity pacing to improve arthritis-related pain and functioning and increase physical activity.
Methods

A randomized feasibility and acceptability pilot trial compared Engage-PA to treatment as usual plus fitness tracker (TAU+) in N=40 adults age 65+ with OA pain in the knee or hip. Engage-PA involved two 60-minute telephone sessions. All participants wore a fitness tracker to collect daily steps throughout the study and completed baseline and post-treatment assessments of secondary outcomes (arthritis-related pain and physical functioning, physical activity, psychological distress, psychological flexibility, and value-guided action). The impact of COVID-19 on general wellbeing and physical activity was also assessed. Descriptive statistics were conducted for feasibility and acceptability outcomes. Indicators of improvement in secondary outcomes were examined via change scores from baseline to post-treatment and performing independent samples t-tests to assess for between-group differences.
Results

Feasibility was high; 100% accrual, low (5%) attrition, and 100% completion of study sessions. Acceptability was high, with 89% finding the intervention “mostly” or “very” helpful. Engage-PA participants demonstrated improvements in arthritis pain severity (Mdiff=1.68, p<.05), arthritis-related physical functioning (Mdiff=.875, p=.056), and self-reported activity (Mdiff=.875, p<.05) from baseline to post-treatment as compared to TAU+. Sixty-three percent of participants provided useable objective daily steps data. Other secondary outcome patterns were not interpretable in this small sample. COVID-19 added additional burden to participants, such that 50% were exercising less, 68% were more sedentary, and 72% lost access to spaces and social support to be active.
Conclusions

Engage-PA is a promising brief, novel behavioral intervention that has potential to support older adults in improving arthritis-related pain and functioning and increasing physical activity. The feasibility and acceptability of the intervention is particularly notable as most participants reported COVID-19 added more barriers to physical activity, and Engage-PA may be appealing in future studies.
Trial Registration:

clinicaltrials.gov, NCT04490395, registered 7/29/2020, https://clinicaltrials.gov/ct2/show/NCT04490395.
A New Multistate Transition Model For Effect Estimation In Randomized Trials With Treatment Switching And A Cured Subgroup
Authors: Hu Haixia , Wang Ling , Li Chen , Ge Wei , Xia Jielai 
Published: January 2022

Abstract
Background: Many methods, including multistate models, have been proposed in the literature to estimate the treatment effect on overall survival in randomized trials with treatment switching permit after the disease progression. Nevertheless, the cured fraction of patients has not been considered. The cured would never experience the progressive disease, but they may suffer death with a hazard comparable to that of people without the disease. With the mix of the cured subgroup, existing methods yield highly biased effect estimation and fail to reflect the truth in uncured patients. Methods: In this paper, we propose a new multistate transition model to incorporate the cure, progression, treatment switching, and death states during trials. In the proposed model, the probability of cure and the death hazard of the cured are modeled separately. For the not cured patients, the semi-competing risks model is used with the treatment effect evaluated via transitional hazards between states. The particle swarm optimization algorithm is adopted to estimate the model parameters. Results: Extensive simulation studies have been conducted to evaluate the performance of the proposed multistate model and compare it with existing treatment switching adjustment methods. Results show that in all scenarios, the treatment effect estimation of the proposed model is more accurate than that of existing treatment switching adjustment methods. Besides, the application to diffuse large B-cell lymphoma data has also illustrated the superiority of the proposed model.Conclusions: The superiority and robustness of the proposed multistate transition model qualify it to estimate the treatment effect in trials with the treatment switching permit after progression and a cured subgroup.
Dephosphorylation of Nitrate Reductase Protein Regulates Growth of Rice and Adaptability to Low Temperature
Authors: Han Ruicai , Li Chenyan , Li Huijie , Wang Yupeng , Pan Xiaohua , Shi Qinghua , Fang Jiahai , Wu Ziming 
Published: January 2022

Abstract
Nitrate reductase (NR) is an important enzyme for nitrate assimilation in plants, and its activity is regulated by post-translational phosphorylation. To investigate the effect of NIA1 protein dephosphorylation on the growth of rice and its adaptability to low temperature, we analyzed phenotype, chlorophyll content, nitrogen utilization, and antioxidant capacity at low temperature in lines with a mutated NIA1 phosphorylation site (S532D and S532A), an OsNia1 over-expression line (OE), and wild-type Kitaake rice (WT). Plant height, dry matter weight, and chlorophyll content of S532D and S532A were lower than those of WT and OE under normal growth conditions but were higher than those of WT and OE at low temperature. Compared with WT and OE, the nitrite, H2O2, and MDA contents of S532D and S532A leaves were higher under normal growth conditions. The difference in leaf nitrite content between transgenic lines and WT was narrower at low temperature, especially in S532D and S532A, while H2O2 and MDA contents of S532D and S532A leaves were lower than those in WT and OE leaves. The NH4+-N and amino acid contents of S532D and S532A leaves were higher than those of WT and OE leaves under normal or low temperature. qRT-PCR results revealed that transcription levels of OsNrt2.4, OsNia2, and OsNADH-GOGAT were positively correlated with those of OsNia1, and the transcription levels of OsNrt2.4, OsNia2, and OsNADH-GOGAT were significantly higher in transgenic lines than in WT under both normal and low temperature. Phosphorylation of NR is a steady-state regulatory mechanism of nitrogen metabolism, and dephosphorylation of NIA1 protein improved NR activity and nitrogen utilization efficiency in rice. Excessive accumulation of nitrite under normal growth conditions inhibits the growth of rice; however, accumulation of nitrite is reduced at low temperature, enhancing the cold tolerance of rice.
Dynamic Alteration in Cerebral Total Hemoglobin Concentration Measured Using Portable Near-infrared Spectroscopy in Orthostatic Hypotension and Intolerance
Authors: Kim Jae-Myoung , Park Kyung-Il , Choi Su-Yeon , Park Hyo Eun , Lee Heesun , Bae Hyeon-Min 
Published: January 2022

Abstract
A portable near infrared spectroscopy (NIRS) system was used to evaluate alterations in cerebral total hemoglobin concentration (HbT) in individuals with orthostatic hypotension (OH) and orthostatic intolerance (OI) symptoms. We enrolled 238 healthy participants (mean age, 47.9 years) and assessed the presence of OH (orthostatic blood pressure (BP) drop of systolic BP ≥ 20 mmHg or diastolic BP ≥ 10 mmHg within 3 minutes of supine-to-stand) and OI symptoms using the OH questionnaire. The participants were categorized into three groups based on the presence of OH and OI symptoms: the classic OH (OH-BP) group, symptom alone (OH-Sx) group, and control group. Random case-control matching sets (age, sex, hypertension, and diabetes mellitus) were constructed consisting of 16 OH-BP and 69 OH-Sx-control sets. We measured the time-derivative of HbT change in the prefrontal cortex during the squat-to-stand maneuver. There were no differences in demographics, baseline BP, and heart rate among the matched sets. Among the NIRS parameters, the peak-time of maximum slope variation was significantly longer in the OH-Sx and OH-BP groups than in the matched control groups during transition to the standing position after squatting. Our results suggested that OH and OI symptoms are associated with dynamic alteration in cerebral HbT.
Microvirga Puerhi Sp. Nov., Isolated from Puerh Tea Garden Soil
Authors: Zi Zhi-Da , Wen Wen , Ma Fu , Li Wei , Wang Zhao-Xuan , Lu Jun , Lv Jie 
Published: January 2022

Abstract
Strain WGZ8T was isolated from a soil sample of Puerh tea garden in Puer city, Southwest China. The isolate was rod-shaped, Gram-stain negative, aerobic, non-motile. Growth occurred within 0-3.0% (w/v) NaCl (optimal concentration, 0-1.0%), pH 5.0-11.0 (optimal pH, 7.0) and 10-40°C (optimal temperature, 28°C). 16S rRNA gene sequences based phylogenetic and phylogenomic analysis revealed that WGZ8T belonged to the genus Microvirga. Its major cellular fatty acids were C19:0 cyclo ω8c, C16:0, C18:1ω7c and/or C18:1ω6c. The profile of polar lipids included phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phosphatidyl-glycerol. The only respiratory quinone was detected as ubiquinone 10 (Q-10). The genome size of strain WGZ8T was 5.17MB, and the content of DNA G+C was 61%. Based on the results of digital DNA-DNA hybridization and phenotypic results, strain WGZ8T could be concluded as a novel species of the genus Microvirga, for which the name Microvirga puerhi sp. nov. is proposed. The type strain is WGZ8T (=CGMCC 1.19171T=JCM XXXXT).
Porous Cellulose-Collagen Scaffolds For Soft Tissue Regeneration: Influence of Cellulose Derivatives On Mechanical Properties And Compatibility With Adipose-Derived Stem Cells.
Authors: Kacvinská Katarína , Trávničková Martina , Vojtová Lucy , Poláček Petr , Dorazilová Jana , Kohoutek Martin , Pajorová Júlia , Tirpáková Mária , Bačáková Lucie 
Published: January 2022

Abstract
This study deals with cellulose derivatives in relation to the collagen fibrils in composite collagen-cellulose scaffolds for soft tissue engineering. Two types of cellulose, i.e., oxidized cellulose (OC) and carboxymethyl cellulose (CMC), were blended with collagen (Col) to enhance its elasticity, stability and sorptive biological properties, e.g. hemostatic and antibacterial features. The addition of OC supported the resistivity of the Col fibrils in a dry environment, while in a moist environment OC caused a radical drop. The addition of CMC reduced the mechanical strength of the Col fibrils in both environments. The elongation of the Col fibrils was increased by both types of cellulose derivatives in both environments, which is closely related to tissue like behaviour. In these various mechanical environments, the ability of human adipose-derived stem cells (hADSCs) to adhere and proliferate was significantly greater in the Col and Col/OC scaffolds than in the Col/CMC scaffold. This is explained by deficient mechanical support and loss of stiffness due to the high swelling capacity of CMC. Although Col/OC and Col/CMC acted differently in terms of mechanical properties, both materials were observed to be cytocompatible, with varying degrees of further support for cell adhesion and proliferation. While Col/OC can serve as a scaffolding material for vascular tissue engineering and for skin tissue engineering, Col/CMC seems to be more suitable for moist wound healing, e.g. as a mucoadhesive gel for exudate removal, since there was almost no cell adhesion.
Survey of Opioid-Induced Respiratory Depression in Critically Ill Patients Without Mechanical Ventilation and Construction of a Risk Nomogram
Authors: Sha Tong , Xuan Jiabin , Li Lulan , Wu Jie , Chen Kerong , Huang Qiaobing , Hu Hongbin , Zhang Yuan , Chen Zhongqing , Zeng Zhenhua 
Published: January 2022

Abstract
Objectives
To investigate the current status of opioid-induced respiratory depression (OIRD) and potential risk factors in critically ill patients without mechanical ventilation in the intensive care unit (ICU) and to construct a risk nomogram to predict OIRD.
Methods
A total of 103 patients without (or who were weaned from) mechanical ventilation who had stayed for more than 24 h in the ICU between June 1, 2021 and September 31, 2021, were included. Patient data, including respiratory depression events, were recorded. The least absolute shrinkage and selection operator regression model were used to select features that were then used to construct a prediction model by multivariate logistic regression analysis. A nomogram was established for the risk of respiratory depression events in patients without mechanical ventilation. The discriminatory performance and calibration of the nomogram were assessed with Harrell’s concordance index and a calibration plot, respectively, and a bootstrap procedure was used for internal validation.
Results
Respiratory depression was diagnosed in 49/103 (47.6%) patients. Factors included in the nomogram were cardiopulmonary disease (odds ratio [OR]=5.569, 95% confidence interval [CI]=0.751–118.083), respiratory disease (OR=32.833, 95% CI=4.189–725.164), sepsis (OR=6.898, 95% CI=1.756–33.000), duration of mechanical ventilation (OR=3.019, 95% CI=0.862–11.322), lack of mechanical ventilation (OR=20.757, 95% CI=2.409–502.222), and oxygenation index (OR=7.350, 95% CI=2.483–24.286). The nomogram showed good performance for predicting respiratory depression events in critically ill patients without mechanical ventilation.
Conclusion
The nomogram can be used to identify ICU patients without mechanical ventilation who are at risk of opioid-induced respiratory depression and may therefore benefit from early intervention.
Draft Genome of Cochliopodium minus (Amoebozoa): Insights into Its Complex Sexual Behavior, Across Domain Gene Acquisitions and Metazoan Type Signaling
Authors: Tekle Yonas I. , Wang Fang , Tran Hanh , Hayes T. Danielle , Ryan Joseph F. 
Published: January 2022

Abstract
To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium’s sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.
Evidence for Shared Neural Information Between Muscle Synergies and Corticospinal Efficacy
Authors: Young David R. , Banks Caitlin L. , McGuirk Theresa E. , Patten Carolynn 
Published: January 2022

Abstract
Stroke survivors often exhibit gait dysfunction which compromises self-efficacy and quality of life. Muscle Synergy Analysis (MSA), derived from electromyography (EMG), has been argued as a method to quantify the complexity of descending motor commands and serve as a direct correlate of neural function. However, controversy remains regarding this interpretation, specifically attribution of MSA as a neuromarker. Here we sought to determine the relationship between MSA and accepted neurophysiological parameters of motor efficacy in healthy controls, high (HFH) and low (LFH) functioning stroke survivors. Surface EMG was collected from twenty-four participants while walking at their self-selected speed. Concurrently, transcranial magnetic stimulation (TMS) was administered, during walking, to elicit motor evoked potentials (MEPs) in the plantarflexor muscles during the pre-swing phase of gait. MSA was able to differentiate control and LFH individuals. Conversely, motor neurophysiological parameters including soleus MEP area, revealed that MEP latency differentiated control and HFH individuals. Significant correlations were revealed between MSA and motor neurophysiological parameters adding evidence to our understanding of MSA as a correlate of neural function and highlighting the utility of combining MSA with other relevant outcomes to aid interpretation of this analysis technique.