bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic yield, safety and impact of transbronchial lung biopsy in mechanically ventilated, critically ill patients: a retrospective study
Authors: Ghiani Alessandro , Neurohr Claus 
Published: October 2020

Abstract
Background: Pulmonary infiltrates of variable etiology are one of the main reasons for hypoxemic respiratory failure leading to invasive mechanical ventilation. If pulmonary infiltrates remain unexplained or progress despite treatment, the histopathological result of a lung biopsy could have significant impact on change in therapy. Surgical lung biopsy is the commonly used technique, but due to its considerable morbidity and mortality, less invasive bronchoscopic transbronchial lung biopsy (TBLB) may be a valuable alternative. Methods: Retrospective, monocentric, observational study in mechanically ventilated, critically ill patients, subjected to TBLB due to unexplained pulmonary infiltrates in the period January 2014 to July 2019. Patients` medical records were reviewed to obtain data on baseline clinical characteristics, modality and adverse events (AE) of the TBLB, and impact of the histopathological results on change in therapy. A multivariable binary logistic regression analysis was performed to identify predictors of AE and hospital mortality, and survival curves were generated using the Kaplan-Meier method. Results: Forty-two patients with in total 42 TBLB procedures after a median of 12 days of mechanical ventilation were analyzed, of which 16.7% were immunosuppressed, but there was no patient with prior lung transplantation. Diagnostic yield of the TBLB was 88.1%, with AE occurring in 11.9% (most common pneumothorax and minor bleeding). 92.9% of the procedures were performed as a forceps biopsy, with organizing pneumonia (OP) being the most common histological diagnosis (54.8%). Variables independently associated with hospital mortality were age (odds ratio 1.070, 95%CI 1.006–1.138; p = 0.031) and the presence of OP (0.182, [0.036–0.926]; p = 0.040), the latter being confirmed in the survival analysis (log-rank p = 0.040). In contrast, a change in therapy based on histopathology alone occurred in only 40.5%, and there was no evidence of a survival benefit in those patients. Conclusions: Transbronchial lung biopsy remains a valuable alternative to surgical lung biopsy in mechanically ventilated critically ill patients. However, the high diagnostic yield must be weighed against potential adverse events and limited consequence of the histological result regarding treatment decisions in such patients.
Predicting Functional Performance via Classification of Lower Extremity Strength in Older Adults with Exergame-Collected Data
Authors: Becker Hagen , Garcia-Agundez Augusto , Müller Philipp Niklas , Tregel Thomas , Miede André , Göbel Stefan 
Published: October 2020

Abstract
Objective: The goal of this article is to present and to evaluate a sensor-based functional performance monitoring system. The system consists of an array of Wii Balance Boards (WBB) and an exergame that estimates whether the player can maintain physical independence, comparing the results with the 30 Second Chair-Stand Test (30CST). Methods: Sixteen participants recruited at a nursing home performed the 30CST and then played the exergame described here as often as desired during a period of two weeks. For each session, features related to walking and standing on the WBBs while playing the exergame were collected. Different classifier algorithms were used to predict the result of the 30CST on a binary basis as able or unable to maintain physical independence. Results: By using a Logistic Model Tree, we achieved a maximum accuracy of 91% when estimating whether player’s 30CST scores were over or under a threshold of 12 points, Our findings suggest that predicting age- and sex-adjusted cutoff scores is feasible. Conclusion: An array of WBBs seems to be a viable solution to estimate lower extremity strength and thereby functional performance in a non-invasive and continuous manner. This study provides proof of concept supporting the use of exergames to identify and monitor elderly subjects at risk of losing physical independence.
Modified Kocher-Langenbeck approach for the treatment of posterior wall or column acetabular fractures: The one-incision two-window method
Authors: Yang Tien-Yu , Huang Kuo-Chin 
Published: October 2020

Abstract
Abstract
The Kocher-Langenbeck (K-L) approach is the standard method for the treatment of posterior wall or column acetabular fractures. This approach allows direct access to the posterior structures of the acetabulum, but is limited cranially and caudally by the neurovascular bundle. The present study was conducted to assess the quality of reduction and the incidence of complications in patients who underwent the modified “one-incision two-window” K-L approach.
Methods : This is a Retrospective case series with recruited thirteen consecutive patients from 2015 to 2017 who sustained an acute, displaced posterior wall or column acetabular fracture. All patients were treated with modified “one-incision two-window” K-L approach.
Results: The mean operation time, mean intraoperative blood loss, and mean incision wound length were estimated to be 103.8 min (60-120 min), 373.1 mL (100-700 mL), and 9.7 cm (8.0-13.0 cm), respectively. The radiographic quality of reduction was graded as anatomical reduction (maximum residual displacement [MRD] ≤ 2 mm) in all cases, according to Matta’s criteria. Concerning the incidence of complications, there were no iatrogenic neurovascular injury, no surgical site infections, and no osteonecrosis of the femoral head or heterotopic ossification in this cohort. One patient with transverse posterior wall fracture (group 1) experienced deep vein thrombosis in the lesion leg. Another two patients with solitary posterior wall fracture (group 2) developed posttraumatic osteoarthritis, with one diagnosed as Tonnis grade I lesion and the other as Tonnis grade III lesion. With respect to the clinical treatment outcome, the mean visual analogue scale (VAS), mean modified Harris Hip Score (mHHS) and subjective satisfaction rate were 1.7 (1.0-2.0), 90.6 (81-100), and 84.6% (80%-90%), respectively. Although there was no significant difference in the satisfaction rate (82.9% vs. 87.0%, P = 0.941) at 12 months after surgery, group 1 patients had more increased VAS score (2.0 vs. 1.2, P = 0.016) and more decreased mHHS (87.7 vs. 94.6, P = 0.014) than group 2 patients.
Conclusions: Our pilot study confirmed that the “one-incision two-window” K-L approach is a simple, safe, reliable, and effective way to manage acute, displaced posterior wall or column acetabular fractures.
A patient satisfaction survey investigating pre- and post-operative information provision in lower limb surgery
Authors: Renna Maxwell Stanley , Metcalfe Andrew , Ellard David , Davies David 
Published: October 2020

Abstract
Background Planned lower limb surgery is common, with over 90,000 hip replacements, 95,000 knee replacements and 15,000 anterior cruciate ligament reconstructions performed in the UK each year. These procedures are primarily indicated to treat osteoarthritis, sporting injuries and trauma. Patient satisfaction is an important element of healthcare provision, which is usually measured by functional outcomes but influenced by other factors. Few studies have assessed patients’ views on the information given to them pertaining surgery and patients are infrequently consulted when designing leaflets and information packs, which can lead to confusion during the recovery period and poor long-term outcomes. Furthermore, previous studies have not directly asked patients what resources they would prefer, or which format would suit them best. This project aimed to assess if patients were satisfied with the information they received around their operations and to identify potential improvements.Methods Set in a National Health Service (NHS) run major trauma centre in the West Midlands, a multiple choice and free-text answer survey was administered to patients who used the orthopaedic service over the course of one month. Surveys were designed in Qualtrics and administered face-to-face on paper. Thematic content analysis was performed on the results. Results Eighty patients completed the survey, of which 88.8% of patients were satisfied with the information they received. Discussions with surgeons were the most useful resource and 53% of patients requested more internet resources. Post-operative patients were statistically more likely to be dissatisfied with information provision than pre-operative patients. Over 20% of study population requested more information on post-operative pain and recovery timelines. Conclusions Although patients were satisfied in general, areas for change were identified. Suggested resources take the form of webpages and mobile platforms. These resources could contain educational videos, patient experience blogs or interactive recovery timelines, to be of benefit to patients. These suggestions may enable NHS Trusts to “get into the digital age”, however, more research on patient satisfaction around information provision and the impact it has on recovery and decision making is needed.
The identification and determination of toxin genes of Vibrio strains causing hemorrhagic disease on red drum (Sciaenops ocellatus) using PCR method
Authors: Linh Nguyen Quang , Pham Yen Thi Hai , Nguyen Tram Duy Quynh 
Published: October 2020

Abstract
Data were collected from 30 strains of Vibrio and sampled on different organs (brain, hemorrhagic site and digestive tract) of Sciaenops ocellatus infection. The results showed that the nucleotide sequences 16S rRNA region are highly similar to those of V. alginolyticus, V. azureus, V. fluvialis, V. natriengens and V. orientalis, which were published on Genbank and other, ranging from 98.05 to 100 %. The digestive tract has the most common Vibrio strains (V. alginolyticus [16] V. azureus [7] and V. fluvialis). Thereout, 25 of 30 strains of Vibrio contained from 1 to 3 toxin genes, except for V. parahaemolyticus. Six parameters were used to measure the DNA polymorphism of 33 homologous DNA sequences in this Vibrio bacteria population. The results indicated that the number of separate polymorphic sites (S), the total number of mutant sites (Eta), the number of haplotype (h), the haplotype diversity (Hd), the average number of nucleotide differences (k), the nucleotide diversity (Pi) were 98 (S), 103 (Eta), 9 (h), 0.887 ± 0.032 (Hd), 25.789 (k) and 17.980x10-3 ± 0.003 (Pi), respectively (P < 0,05). The G+C contentover 1434 sites positions of nucleotide sequences accounted for 0.542. The phylogenetic tree showed that these strains are divided into six groups. As observed, the appearance of isolated Vibrio on 3 organs of fish (S. ocellatus) which are hemorrhagic include V. azureus (27,67 %), V. alginolyticus (50 %), V. orientalis (6,67 %) and V. fluvialis (16,67 %). Through this result, it is found that the diversity of Vibrio species that appeared on the red drum was used in the 16S rRNA region and the presence of toxin genes in these Vibrio species.
Morphology, genetic characterization and molecular phylogeny of pinworm Skrjabinema longicaudatum sp. n. (Oxyurida: Oxyuridae) from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae)
Authors: Cao Yi-Fan , Chen Hui-Xia , Li Yang , Zhou Dang-Wei , Chen Shi-Long , Li Liang 
Published: October 2020

Abstract
Background: The Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae) is an endangered species of mammal endemic to the Qinghai-Tibetan Plateau. Parasites and parasitic diseases are considered to be important threats in the conservation of the Tibetan antelope. However, our present knowledge of the composition of the parasites of the Tibetan antelope remains limited. Methods: Large numbers of nematode parasites were collected from a dead Tibetan antelope. The morphology of these nematode specimens was observed using light and scanning electron microscopy. The nuclear and mitochondrial DNA sequences, i.e. small subunit ribosomal DNA (18S), large subunit ribosomal DNA (28S), internal transcribed spacer (ITS) and cytochrome c oxidase subunit 1 (cox1), were amplified and sequenced for molecular identification. Moreover, phylogenetic analyses were performed using maximum likelihood (ML) inference based on 28S and 18S + 28S + cox1 sequence data, respectively, in order to clarify the systematic status of these nematodes.Results: Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of pinworm Skrjabinema longicaudatum (Oxyurida: Oxyuridae). There was no intraspecific nucleotide variation between different individuals of S. longicaudatum n. sp. in the partial 18S, 28S, ITS and cox1 sequences. However, a high level of nucleotide divergence was revealed between the new species and its congeners in 28S (8.36%) and ITS (20.3–23.7%) regions, respectively. Molecular phylogenetic results suggest that the genus Skrjabinema should belong to the subfamily Oxyurinae (Oxyuroidea: Oxyuridae), instead of the subfamily Syphaciidae or Skrjabinemiinae in the traditional classification, as it formed a sister relationship to the genus Oxyuris. Conclusions: A new species of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) is described. Skrjabinema longicaudatum n. sp. represents the first species of Oxyurida (pinworm) and the fourth nematode species reported from the Tibetan antelope. Our results contribute to the knowledge of the species diversity of parasites from the Tibetan antelope, and clarify the systematic position of the genus Skrjabinema.
Hemopneumothorax Detection Through the Process of Artificial Evolution - A Feasibility Study
Authors: Sommer Adir , Mark Noy , Gerasi Rafi , Avraham Linn Wagnert , Fan-Marko Ruth , Eisenkraft Arik , Nachman Dean 
Published: October 2020

Abstract
Background: Tension pneumothorax is one of the leading causes of preventable death on the battlefield. Current prehospital diagnosis relies on a subjective clinical impression complemented by a manual thoracic and respiratory examination. These techniques are not fully applicable in field conditions and on the battlefield, where situational and environmental factors may impair clinical capabilities. We aimed to assemble a device able to sample, analyze, and classify the unique acoustic signatures of pneumothorax and hemothorax. Methods: Tested on an ex-vivo porcine model, we have assembled a device consisting of two sensitive digital stethoscopes and sampled 12 seconds of mechanical ventilation breathing sounds over the animals’ thorax. The thoracic cavity was injected with increasing volumes of 200, 400, 600, 800, and 1000 ml of air and saline to simulate pneumothorax and hemothorax, respectively. The data was analyzed using a multi-objective genetic algorithm that was used to develop an optimal mathematical detector through the process of artificial evolution, a cutting-edge approach in the artificial intelligence discipline. Results: The algorithm was able to classify the signals according to their distinctive characteristics and to accurately predict, in up to 80% of cases, the presence of pneumothorax and hemothorax, starting from 400 ml, and regardless of background noise.Conclusions: We present a potential objective and rapid diagnosis modality that can overcome independent and subjective factors that may delay diagnosis and treatment of potentially lethal thoracic injuries, with emphasis on field conditions. A future diagnostic device could be embedded with the algorithm and provide real-time detection and monitoring of pneumothorax and hemothorax.
Low neoantigen expression and poor T cell priming underlie early immune escape in cancer
Authors: Westcott Peter , Sacks Nathan , Schenkel Jason , Smith Olivia , Zhang Daniel , Hauck Haley , Backlund Coralie , Beytagh Mary , Patten JJ , Eng George , Irvine Darrell , Yilmaz Ömer , Jacks Tyler 
Published: October 2020

Abstract
Immune evasion is a hallmark of cancer, and therapies that restore immune surveillance have proven highly effective in cancers with high tumor mutation burden (TMB) (e.g. microsatellite instable (MSI) colorectal cancer (CRC)). Whether low TMB cancers, which are largely refractory to immunotherapy, harbor T cell neoantigens capable of engaging adaptive immunity remains unclear. Here, we show that the majority of microsatellite stable (MSS) CRC harbors predicted high-affinity neoantigens despite low TMB. Unexpectedly, these neoantigens are broadly expressed at lower levels relative to those in MSI CRC, suggesting a potential role of antigen expression in tumor immune surveillance. To test this, we developed a versatile platform for functional interrogation of neoantigens with variable expression and applied it to novel preclinical colonoscopy-guided mouse models of CRC. While high expression of multiple high-affinity MHC-I-restricted neoantigens universally resulted in tumor rejection, low expression resulted in poor T cell priming and tumor progression. Strikingly, experimental or therapeutic rescue of priming rendered T cells fully capable of controlling tumors with low neoantigen expression. These findings underscore a critical role of neoantigen expression levels in immune evasion and suggest that poor expression or presentation may be a general feature of neoantigens acquired early in tumorigenesis. Finally, poorly expressed neoantigens, commonly excluded in tumor vaccine pipelines, may hold untapped therapeutic potential.
Assessment of the effectiveness of pain management among trauma patients in the emergency department
Authors: Wazzan Ahmad , Albeladi Yazeed Khalid , Altaifi Rozan Ibrahim , Alqahtani Mohammed Saeed , Bakheet Rayan Mahmoud 
Published: October 2020

Abstract
Background:In the emergency department (ED), pain is the most common complaint, especially among trauma patients. However, two-thirds of trauma patients are discharged from EDs with moderate to severe pain. Therefore, pain management is an important part of care in ED's trauma patients.Aim:To assess the effectiveness of pain management among trauma patients in the ED.Method:A retrospective cohort study that was conducted on adult trauma patients who attended the ED at King Abdulaziz medical city (KAMC) in Jeddah from the period (June 2016 to July 2018). The pain was measured twice, one before the intervention and one after intervention using a numeric pain scale. Data were collected from health information system (Best care®) and analyzed using SPSS version 24.Results:The Mean difference between pain scores before and after pain management was one on a numeric pain scale with a P-Value 0.001. Initial pain assessment occurred only in 69% of our population, while assessment after intervention happened in 71% of patients. Patients who received appropriate medication were 36.7%. 35% of patients received opioids as an initial drug of pain management; only 8.8% of patients had pain scores more than 7 initially. The median between the time of arrival and the time of Initial Assessment is 19 mins.Conclusion:Pain management in ED needs improvement. Timeliness of pain management should be addressed. Evaluation and re-evaluation of pain before and after the intervention is insufficient. Trauma Patients don't receive effective pain management in the ED.
MICRA-Net: MICRoscopy Analysis Neural Network to solve detection, classification, and segmentation from a single simple auxiliary task
Authors: Lavoie-Cardinal Flavie , Bilodeau Anthony , Delmas Constantin , Parent Martin , Koninck Paul De , Durand Audrey 
Published: October 2020

Abstract
High throughput quantitative analysis of microscopy images presents a challenge due to the complexity of the image content and the difficulty to retrieve precisely annotated datasets. In this paper we introduce a weakly-supervised MICRoscopy Analysis neural network (MICRA-Net) that can be trained on a simple main classification task using image-level annotations to solve multiple more complex auxiliary tasks, such as segmentation, detection, and enumeration. MICRA-Net relies on the latent information embedded within a trained model to achieve performances similar to state-of-the-art fully-supervised learning. This learnt information is extracted from the network using gradient class activation maps, which are combined to generate precise feature maps of the biological structures of interest. We demonstrate how MICRA-Net significantly alleviates the expert annotation process on various microscopy datasets and can be used for high-throughput quantitative analysis of microscopy images.
Mechanical Removal of Surface Residues on Graphene for TEM Characterizations
Authors: KIM Dong-Gyu , Lee Sol , Kim Kwanpyo 
Published: October 2020

Abstract
Contamination on two-dimensional (2D) crystal surfaces poses serious limitations on fundamental studies and applications of 2D crystals. Surface residues induce uncontrolled doping and charge carrier scattering in 2D crystals, and trapped residues in mechanically assembled 2D vertical heterostructures often hinder coupling between stacked layers. Developing a process that can reduce the surface residues on 2D crystals is important. In this study, we explored the use of atomic force microscopy (AFM) to remove surface residues from 2D crystals. Using various transmission electron microscopy (TEM) investigations, we confirmed that surface residues on graphene samples can be effectively removed via contact-mode AFM scanning. The mechanical cleaning process dramatically increases the residue-free areas, where high-resolution imaging of graphene layers can be obtained. We believe that our mechanical cleaning process can be utilized to prepare high-quality 2D crystal samples with minimum surface residues.
Interferon Gamma Release Assay After BCG Vaccination Among Newborns and Family Members Living in an Overcrowded Area in Jakarta, Indonesia
Authors: Tanoerahar Francisca Srioetami , Rooslamiati Indri , Kipuw Natalie , Hadiyanto  , Ali Soegianto , Sahiratmadja Edhyana 
Published: October 2020

Abstract
IntroductionActive tuberculosis (TB) patient is a potential source of Mycobacterium tuberculosis transmission in an overcrowded and poor area. Family members living in the same house may have been infected or latent tuberculosis infection (LTBI) may develop. The aim of the study was to explore LTBI among newborns and their family members living in an overcrowded area in Jakarta, Indonesia. MethodsA prospective analytical study was conducted among newborns from October 2016 to March 2017. Interferon gamma release assay (IGRA) was examined before BCG vaccination and after 12 weeks. In parallel, TB active case finding was performed among family members of the newborns.ResultsOf 135 newborns, only 117 (86.7%) came for BCG vaccination. Of 346 family members screened, 8 (2.3%) were detected as untreated active pulmonary TB, confirmed by positive sputum and/or MTB culture. Family members living in the same house with active TB individuals (p=0.011, OR 2.69) as well as being males (p = 0.025; OR 1.68) had a significant higher risk of having a positive IGRA. ConclusionsUntreated pulmonary TB infection in overcrowded areas infects the surrounding neighbors, resulting in latent TB infection. An active program for detecting pulmonary TB cases and preventive measures need to be taken seriously to contain the potential spreading of the infection.