bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delayed laparoscopic peritoneal washout in non-operative management of blunt abdominal trauma: a scoping review
Authors: Chu Megan , How Nathan , Laviolette Alysha , Bilic Monika , Tang Jennifer , Khalid Maham , Bos Cecily , Rice Timothy J. , Engels Paul T. 
Published: July 2022

AbstractObjectivesNon-operative management (NOM) of blunt abdominal trauma has become increasingly common in hemodynamically stable patients. There are known complications of NOM from undrained intra-abdominal fluid accumulations including hemorrhage and peritonitis that require delayed operation. Thus, delayed operation can be considered as part of the overall management plan, instead of failure, of NOM. The aim of this scoping review is to establish key concepts regarding delayed laparoscopic peritoneal washout (DLPW) following NOM of blunt abdominal trauma patients.MethodsMEDLINE, EMBASE, CENTRAL, and gray literature were systematically searched. Studies were included if they investigated or reported on the use of delayed laparoscopy involving peritoneal washout following NOM of blunt abdominal trauma patients. Bibliographies of included studies were manually reviewed to identify additional articles for inclusion.ResultsFrom 910 citations, 28 studies met inclusion criteria. This included seven case reports, eleven case series or observational cohort studies, six review articles, two management guidelines, one textbook chapter, and one randomized clinical trial. For those reported, medium grade liver injuries proved most common (95.2%). Indications for DLPW were primarily clinical features and changes in imaging findings, highlighting the importance of close observation. Authors reported clinical improvement after DLPW regarding symptomatology, vital signs, and biochemistry. A relatively high transfusion demand was reported with a mean of four units of packed red blood cells pre-operatively. Length of stay and post-operative complications were consistent with previously reported experiences with blunt abdominal injuries.ConclusionsDLPW is beneficial in blunt abdominal trauma patients following NOM with improvement in symptoms, SIRS features, and a possible reduction in hospital length of stay. This study is limited by low-quality evidence and skewing of data toward isolated hepatic injuries. Future prospective cohort study comparing NOM with and without DLPW is required.
Response to PEEP in COVID-19 ARDS patients with and without extracorporeal membrane oxygenation. A multicenter case–control computed tomography study
Authors: Richard Jean-Christophe , Sigaud Florian , Gaillet Maxime , Orkisz Maciej , Bayat Sam , Roux Emmanuel , Ahaouari Touria , Davila Eduardo , Boussel Loic , Ferretti Gilbert , Yonis Hodane , Mezidi Mehdi , Danjou William , Bazzani Alwin , Dhelft Francois , Folliet Laure , Girard Mehdi , Pozzi Matteo , Terzi Nicolas , Bitker Laurent 
Published: July 2022

AbstractBackgroundPEEP selection in severe COVID-19 patients under extracorporeal membrane oxygenation (ECMO) is challenging as no study has assessed the alveolar recruitability in this setting. The aim of the study was to compare lung recruitability and the impact of PEEP on lung aeration in moderate and severe ARDS patients with or without ECMO, using computed tomography (CT).MethodsWe conducted a two-center prospective observational case–control study in adult COVID-19-related patients who had an indication for CT within 72 h of ARDS onset in non-ECMO patients or within 72 h after ECMO onset. Ninety-nine patients were included, of whom 24 had severe ARDS under ECMO, 59 severe ARDS without ECMO and 16 moderate ARDS.ResultsNon-inflated lung at PEEP 5 cmH2O was significantly greater in ECMO than in non-ECMO patients. Recruitment induced by increasing PEEP from 5 to 15 cmH2O was not significantly different between ECMO and non-ECMO patients, while PEEP-induced hyperinflation was significantly lower in the ECMO group and virtually nonexistent. The median [IQR] fraction of recruitable lung mass between PEEP 5 and 15 cmH2O was 6 [4–10]%. Total superimposed pressure at PEEP 5 cmH2O was significantly higher in ECMO patients and amounted to 12 [11–13] cmH2O. The hyperinflation-to-recruitment ratio (i.e., a trade-off index of the adverse effects and benefits of PEEP) was significantly lower in ECMO patients and was lower than one in 23 (96%) ECMO patients, 41 (69%) severe non-ECMO patients and 8 (50%) moderate ARDS patients. Compliance of the aerated lung at PEEP 5 cmH2O corrected for PEEP-induced recruitment (CBABY LUNG) was significantly lower in ECMO patients than in non-ECMO patients and was linearly related to the logarithm of the hyperinflation-to-recruitment ratio.ConclusionsLung recruitability of COVID-19 pneumonia is not significantly different between ECMO and non-ECMO patients, with substantial interindividual variations. The balance between hyperinflation and recruitment induced by PEEP increase from 5 to 15 cmH2O appears favorable in virtually all ECMO patients, while this PEEP level is required to counteract compressive forces leading to lung collapse. CBABY LUNGis significantly lower in ECMO patients, independently of lung recruitability.
Proteomic response of Turicibacter bilis MMM721 to chicken bile and its bile acids
Authors: Maki Joel J. , Lippolis John D. , Looft Torey 
Published: July 2022

AbstractObjectiveBile and its individual components, mainly bile acids, are important for digestion and drive bacterial community dynamics in the upper gastrointestinal tract of chickens. However, specific responses to bile acids have been characterized in only a few commensal bacteria, and it is unclear how other members of the microbiota respond to biliary stress. Here, we used label-free LC–MS/MS to assess the proteomic response of a common inhabitant of the chicken small intestine,Turicibacter bilisMMM721, to 24 h of growth in anaerobic growth media supplemented with 0.1% whole chicken bile, 0.1% taurochenodeoxycholic acid (TCDCA), or 0.1% taurocholic acid (TCA).ResultsSeventy, 46, and 10 differentially expressed proteins were identified inTuricibacter bilisMMM721 cultured with supplements of chicken bile, TCDCA, and TCA, respectively, when compared to unsupplemented controls. Many differentially expressed proteins were predicted to be involved in ribosomal processes, post-translational modifications and chaperones, and modifications to the cell surface. Ultimately, theT. bilisMMM721 response to whole bile and bile acids is complex and may relate to adaptations for small intestine colonization, with numerous proteins from a variety of functional categories being impacted.
Coexistence of cutaneous endometriosis and ovarian endometrioma: a case report
Authors: Mohaghegh Fatemeh , Hatami Parvaneh , Rajabi Parvin , Aryanian Zeinab 
Published: July 2022

Abstract
Background
Umbilical endometriosis is a rare entity accounting for 0.5–4% of cases with endometriosis.

Case presentation
Here we report a rare case of umbilical endometriosis with concurrent ovarian endometriomas in a 37-year old primiparous Iranian woman.

Conclusion
This interesting coexistence reflects the importance of thorough gynecological assessment in patients with cutaneous endometriosis to enable appropriate management.
High-throughput muscle fiber typing from RNA sequencing data
Authors: Oskolkov Nikolay , Santel Malgorzata , Parikh Hemang M. , Ekström Ola , Camp Gray J. , Miyamoto-Mikami Eri , Ström Kristoffer , Mir Bilal Ahmad , Kryvokhyzha Dmytro , Lehtovirta Mikko , Kobayashi Hiroyuki , Kakigi Ryo , Naito Hisashi , Eriksson Karl-Fredrik , Nystedt Björn , Fuku Noriyuki , Treutlein Barbara , Pääbo Svante , Hansson Ola 
Published: July 2022

Abstract
Background
Skeletal muscle fiber type distribution has implications for human health, muscle function, and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these studies. Here, we present a method based on muscle tissue RNA sequencing data (totRNAseq) to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for a larger number of individuals to be tested.

Methods
By using single-nuclei RNA sequencing (snRNAseq) data as a reference, cluster expression signatures were produced by averaging gene expression of cluster gene markers and then applying these to totRNAseq data and inferring muscle fiber nuclei type via linear matrix decomposition. This estimate was then compared with fiber type distribution measured by ATPase staining or myosin heavy chain protein isoform distribution of 62 muscle samples in two independent cohorts (n = 39 and 22).

Results
The correlation between the sequencing-based method and the other two were rATPas = 0.44 [0.13–0.67], [95% CI], and rmyosin = 0.83 [0.61–0.93], with p = 5.70 × 10–3 and 2.00 × 10–6, respectively. The deconvolution inference of fiber type composition was accurate even for very low totRNAseq sequencing depths, i.e., down to an average of ~ 10,000 paired-end reads.

Conclusions
This new method (https://github.com/OlaHanssonLab/PredictFiberType) consequently allows for measurement of fiber type distribution of a larger number of samples using totRNAseq in a cost and labor-efficient way. It is now feasible to study the association between fiber type distribution and e.g. health outcomes in large well-powered studies.
Ten actions to achieve gender equity among intensivists: the French Society of Intensive Care (FICS) model
Authors: Hamzaoui Olfa , Boissier Florence , Salmon Gandonnière Charlotte , Aubron Cécile , Bodet-Contentin Laetitia , Fartoukh Muriel Sarah , Faure Mélanie , Jourdain Mercedes , Le Marec Julien , Tamion Fabienne , Terzi Nicolas , Hauw-Berlemont Caroline , Aissaoui Nadia ,   FEMMIR Group for the SRLF Trial Group
Published: July 2022

AbstractIn our recent survey, we aimed to collect information on perceived inequity as well as professional and personal fulfillment among women intensivists in France. For the 371 respondents out of the 732 persons who received the survey, the findings were unequivocal: for one-third of the respondents, being a woman was considered as an obstacle to careers or academic advancement, and for two thirds, pregnancy was viewed as a barrier to their career advancement. Gender discrimination had been experienced by 55% of the respondents. In 2019, to promote and achieve gender equity in the French Intensive Care Society (FICS), ten actions were initiated and are detailed in the present manuscript together with supporting data: (1) creation of a working group: the FEMMIR group; (2) promotion of mentorship; (3) implementation of concrete sponsorship; (4) transparency and public reporting of gender ratios in editorial boards; (5) workshops dedicated to unconscious gender bias; (6) workshops dedicated to improved women assertiveness; (7) role models; (8) creation of educational/information programs for young intensivists; (9) development of research on gender inequity and, as a perspective; and (10) development of a wide-ranging program. This review is aimed at providing a toolbox of organizational best practices designed to achieve gender equity. It is particularly important to share promising practical action engaged in our FEMMIR group with other concerned professionals around the world.
CDK6 is upregulated and may be a potential therapeutic target in enzalutamide-resistant castration-resistant prostate cancer
Authors: Chen Xi , Wu Yechen , Wang Xinan , Xu Chengdang , Wang Licheng , Jian Jingang , Wu Denglong , Wu Gang 
Published: July 2022

Abstract
Background
Androgen deprivation therapy (ADT) is still the first-line treatment of prostate cancer (PCa). However, after a certain period of therapy, primary PCa inevitably progresses into castration-resistant PCa (CRPC). Enzalutamide (Enz) is an androgen receptor (AR) signal inhibitor which can delay the progression of CRPC and increase survival of patients with metastatic CRPC. However, the mechanisms involved in enzalutamide-resistant (EnzR) CRPC are still controversial. In the study, we used bioinformatic methods to find potential genes that correlated with the occurrence of EnzR CRPC.

Methods
We collected RNA sequencing data of the EnzR CRPC cell line LNCaP (EnzR LNCaP) from GSE44905, GSE78201, and GSE150807. We found the hub genes from the three datasets. Then we tested the expression of the hub genes in different databases and the potential drugs that can affect the hub genes. Finally, we verified the hub gene expression and drug function.

Results
From GSE44905, GSE78201 and GSE150807, we found 45 differentially expressed genes (DEGs) between LNCaP and EnzR LNCaP. Ten hub genes were found in the protein–protein interaction (PPI) network. The expression of hub gene and survival analysis were analyzed by different databases. We found that cyclin-dependent kinase 6 (CDK6) was highly expressed in both the EnzR LNCaP cell and PCa patients. Ten potential small molecules could suppress CDK6 expression as per “CLUE COMMAND” findings. Finally, we found the expression of CDK6 increased in both PCa patients’ samples, CRPC and EnzR PCa cell lines. Three potential CDK6 inhibitors, namely apigenin, chrysin and fisetin, can decrease cell proliferation.

Conclusions
The study proved that the abnormal overexpression of CDK6 may be a reason behind EnzR CRPC occurrence and suppression CDK6 expression may help treat EnzR CRPC.
A phase Ib dose-escalation study of troriluzole (BHV-4157), an oral glutamatergic signaling modulator, in combination with nivolumab in patients with advanced solid tumors
Authors: Silk Ann W. , Saraiya Biren , Groisberg Roman , Chan Nancy , Spencer Kristen , Girda Eugenia , Shih Weichung , Palmeri Marisa , Saunders Tracie , Berman Robert M. , Coric Vlad , Chen Suzie , Zloza Andrew , Vieth Joshua , Mehnert Janice M. , Malhotra Jyoti 
Published: July 2022

Abstract
Background
Glutamate signaling activates MAPK and PI3K/AKT pathways in tumor cells. Treatment with riluzole, a glutamate release inhibitor, has been previously shown to be safe in melanoma patients and produced biologic effects, but did not lead to radiographic responses, possibly due to poor pharmacokinetic properties. Therefore, we conducted a phase Ib trial to determine the safety and tolerability of the combination of the riluzole prodrug troriluzole (BHV-4157, trigriluzole) and the PD-1 antibody nivolumab in patients with advanced solid tumors.

Methods
Patients with advanced or refractory solid tumors and measurable disease per RECIST 1.1 were treated with increasing doses of troriluzole using a semi-Bayesian modified toxicity probability interval dose escalation procedure. Troriluzole monotherapy was orally self-administered for a 14-day lead-in period followed by continuation of troriluzole in combination with nivolumab 240 mg IV every 2 weeks. Endpoints included safety, pharmacokinetics (PK) and efficacy.

Results
We enrolled 14 patients with advanced solid tumors (melanoma = 3, NSCLC = 3, renal cell carcinoma = 2, bladder/urothelial = 2, ovarian cancer = 1, adenoid cystic carcinoma = 1, pleural mesothelial = 1, head and neck cancer = 1). Eleven patients had cancer progression on prior therapy with PD-1 or PD-L1 agent. Patients received troriluzole total daily doses from 140 to 560 mg (divided). The most common treatment-related adverse events (TRAE) occurring in ≥ 5 patients (> 35%) were transaminitis and increased lipase. DLT (dose-limiting toxicity) occurred in 3 patients: (1) grade 3 anorexia, (2) grade 3 fatigue and, (3) grade 3 atrial fibrillation. Six patients were treated at the MTD (maximum tolerated dose). No subjects discontinued treatment due to AEs. One response occurred (7%), which was a partial response in a subject who had PD-1 refractory disease. The 6-month PFS rate was 21%. PK data showed that the prodrug troriluzole was efficiently cleaved into riluzole by 2-h post-dosing in all dose cohorts tested.

Conclusion
The combination of troriluzole and nivolumab was safe and well-tolerated. The MTD of troriluzole was determined to be 420 mg total daily dose. The observed antitumor activity, primarily disease stabilization, is of interest in patients with PD-1 resistant tumors.
Trial Registration ClinicalTrials.gov Identifier NCT03229278.
Evaluation of l-arginine supplement on the growth rate, biofilm formation, and antibiotic susceptibility in Streptococcus mutans
Authors: Vaziriamjad Samaneh , Solgi Mobina , Kamarehei Farideh , Nouri Fatemeh , Taheri Mohammad 
Published: July 2022

Abstract
Introduction
Bacteria associated with dental caries have a high ability to produce organic acids from dietary carbohydrates during growth and metabolism under acidic conditions. In contrast, many symbiotic bacteria produce ammonia through the arginine deiminase (ADS) system, which modulates the pH of the oral cavity. l-Arginine metabolism by ADS is a significant inhibitor in the progression of tooth decay. This study aimed to investigate the effect of l-arginine on growth, biofilm formation, and antibiotic susceptibility in Streptococcus mutans.

Methods
In this study, the effect of l-arginine in different concentrations on the growth rate, antibiotic susceptibility, and inhibition of biofilm formation in S. mutans was investigated.

Results
The bacterial exponential growth rate was enhanced by 100 μM l-arginine (P > 0.05). The growth inhibition zone diameter of CAZ, CTR, AMP, and AMC-Clav antibiotics was reduced after 24 h of exposure in the presence of various concentrations of l-arginine specifically at 100 μM. l-Arginine also enhanced biofilm development at 5 and 10 μM concentrations, but reduced it at 50 and 100 μM concentrations.

Conclusion
According to the results of the present study, optimization of l-arginine concentration and its use as an adjunctive therapy or in combination with mouthwash or varnish is recommended to prevent oral caries.
A methodology to assess and improve the physics consistency of an artificial neural network regression model for engineering applications
Authors: Rajasekhar Nicodemus E. 
Published: July 2022

AbstractIn recent times, artificial neural networks (ANNs) have become the popular choice of model for researchers while performing regression analysis between inputs and output. However; in scientific and engineering applications, developed ANN regression model is often found to be inconsistent with the physical laws. This is due to the fact that ANNs are purely based on data and do not have any understanding of underlying physical laws. Alternate ANN frameworks like PGNN (Physics guided neural network) has been proposed in literature which incorporate physics loss function in the overall loss function to partially alleviate this issue. However, these frameworks don’t evaluate the physics consistency of relationship between inputs and output mapped by the ANN model which is the source of all physics inconsistencies. Hence, the present paper presents a methodology to assess and improve the physics consistency of the input output relationship mapped by the ANN regression model. The developed methodology can therefore be used to develop physics consistent ANN regression model. The heart of the methodology is an inferencing algorithm which interprets the input output relationship mapped by the ANN regression model. The inferencing algorithm is based on Taylor series and decomposes the ANN regression model into several region-wise polynomial models. Moreover, the inferencing algorithm can also find regions of singular zones in the ANN model predictions. The region-wise polynomial from inferencing algorithm can be used to assess the physics consistency of the ANN model. In the region of physics inconsistency, additional data points can be added and the ANN model can be re-trained. In cases, where the addition of data points is not possible, a physics based loss function can be used. The developed methodology is illustrated using several datasets. The developed methodology will help engineers and researchers built physics consistent ANN regression models.
Identification of the high-yield monacolin K strain from Monascus spp. and its submerged fermentation using different medicinal plants
Authors: Chen Yu-Pei , Wu Hong-Tan , Hwang Ing-Er , Chen Fang-Fang , Yao Jeng-Yuan , Yin Yiling , Chen Meng-Yun , Liaw Li-Ling , Kuo Yang-Cheng 
Published: July 2022

Abstract
Background
Medical plants confer various benefits to human health and their bioconversion through microbial fermentation can increase efficacy, reduce toxicity, conserve resources and produce new chemical components. In this study, the cholesterol-lowering monacolin K genes and content produced by Monascus species were identified. The high-yield monacolin K strain further fermented with various medicinal plants. The antioxidant and anti-inflammatory activities, red pigment and monacolin K content, total phenolic content, and metabolites in the fermented products were analyzed.

Results
Monacolin K was detected in Monascus pilosus (BCRC 38072), and Monascus ruber (BCRC 31533, 31523, 31534, 31535, and 33323). It responded to the highly homologous mokA and mokE genes encoding polyketide synthase and dehydrogenase. The high-yield monacolin K strain, M. ruber BCRC 31535, was used for fermentation with various medicinal plants. A positive relationship between the antioxidant capacity and total phenol content of the fermented products was observed after 60 days of fermentation, and both declined after 120 days of fermentation. By contrast, red pigment and monacolin K accumulated over time during fermentation, and the highest monacolin K content was observed in the fermentation of Glycyrrhiza uralensis, as confirmed by RT-qPCR. Moreover, Monascus-fermented medicinal plants including Paeonia lactiflora, Alpinia oxyphylla, G. uralensis, and rice were not cytotoxic. Only the product of Monascus-fermented G. uralensis significantly exhibited the anti-inflammatory capacity in a dose-dependent manner in lipopolysaccharide-induced Raw264.7 cells. The metabolites of G. uralensis with and without fermentation (60 days) were compared by LC/MS. 2,3-Dihydroxybenzoic acid, 3,4-dihydroxyphenylglycol, and 3-amino-4-hydroxybenzoate were considered to enhance the antioxidant and anti-inflammatory ability.

Conclusions
Given that highly homologous monacolin K and citrinin genes can be observed in Monascus spp., monacolin K produced by Monascus species without citrinin genes can be detected through the complementary methods of PCR and HPLC. In addition, the optimal fermentation time was important to the acquisition of antioxidants, red pigment and monacolin K. These bioactive substances were significantly affected by medicinal plants over fermentation time. Consequently, Monascus-fermented G. uralensis had a broad spectrum of biological activities.