bluuebunny/crossref_metadata_2025_split huggingface dataset:
The accuracy and effectiveness of automatic pedicle screw trajectory planning based on computer tomography values: an in vitro osteoporosis model study
Authors: Liu Jia Bin , Zuo Rui , Zheng Wen Jie , Li Chang Qing , Zhang Chao , Zhou Yue 
Published: February 2022

Abstract
Background
Pedicle screw placement in patients with osteoporosis is a serious clinical challenge. The bone mineral density (BMD) of the screw trajectory has been positively correlated with the screw pull-out force, while the computer tomography (CT) value has been linearly correlated with the BMD. The purpose of this study was to establish an in vitro osteoporosis model and verify the accuracy and effectiveness of automated pedicle screw planning software based on CT values in this model.

Methods
Ten vertebrae (L1-L5) of normal adult pigs were randomly divided into decalcification and control groups. In the decalcification group, the vertebral bodies were decalcified with Ethylenediaminetetraacetic acid (EDTA) to construct an in vitro osteoporosis model. In the decalcification group, automatic planning (AP) and conventional manual planning (MP) were used to plan the pedicle screw trajectory on the left and right sides of the pedicle, respectively, and MP was used on both sides of the control group. CT values of trajectories obtained by the two methods were measured and compared. Then, 3D-printed guide plates were designed to assist pedicle screw placement. Finally, the pull-out force of the trajectory obtained by the two methods was measured.

Results
After decalcification, the BMD of the vertebra decreased from − 0.03 ± 1.03 to − 3.03 ± 0.29 (P < 0.05). In the decalcification group, the MP trajectory CT value was 2167.28 ± 65.62 Hu, the AP trajectory CT value was 2723.96 ± 165.83 Hu, and the MP trajectory CT value in the control group was 2242.94 ± 25.80 Hu (P < 0.05). In the decalcified vertebrae, the screw pull-out force of the MP group was 48.6% lower than that of the control group (P < 0.05). The pull-out force of the AP trajectory was 44.7% higher than that of the MP trajectory (P < 0.05) and reached 97.4% of the MP trajectory in the control group (P > 0.05).

Conclusion
Automatic planning of the pedicle screw trajectory based on the CT value can obtain a higher screw pull-out force, which is a valuable new method of pedicle screw placement in osteoporotic vertebre.
Analysis of risk factors for multidrug-resistant organisms in diabetic foot infection
Authors: Yan Xi , Song Jin-fang , Zhang Liang , Li Xia 
Published: February 2022

AbstractBackgroundTo study the bacteriological characteristics, risk factors, and treatment of multi-drug resistance (MDR) organisms in patients with diabetic foot infection.MethodsPatients with diabetic foot ulcer admitted to hospital from June 2018 to December 2019 (n = 180) were selected as clinical subjects. Demographic information, routine blood test, wound culture and sensitivity were collected. Risk factors of MDR bacteria were analyzed.ResultsAmong 180 patients with diabetic foot ulcer, 146 were positive in bacterial culture, with 84 positive in MDR bacteria. A total of 182 strains were isolated, with 104 strains being multi-drug resistant. Body mass index, glycosylated hemoglobin, fasting blood glucose, triglyceride, course of ulcer, size of ulcer, peripheral neuropathy, peripheral vascular disease, osteomyelitis, peripheral blood leukocyte count, percentage of neutrophils, and previous use of antibiotics were the related factors of infection of MDR bacteria in diabetic foot ulcer patients (P < 0.05). The leukocyte count and neutrophil ratio of MDR-bacilli were lower than those of non MDR-bacilli (P < 0.05).ConclusionThe risk of MDR bacteria in diabetic foot infection is high. It is necessary to evaluate the risk of multidrug-resistant bacteria by characterizing the course of disease, metabolic control, local ulcer and other aspects in order to formulate an effective treatment plan. The decrease of leukocyte count and neutrophil ratio may be related to damage of the host immune response.
High AKAP8L expression predicts poor prognosis in esophageal squamous cell carcinoma
Authors: Luo Qiu-yun , Di Tian , Qiu Miao-Zhen , Xia Zeng-fei , Du Yong , Lin Run-duan , Yang Li-qiong , Sun Yu-ting , Yang Da-Jun , Sun Jian , Zhang Lin 
Published: February 2022

Abstract
Background
Esophageal squamous cell carcinoma (ESCC) is a severe disease with high mortality, and is associated with poor prognosis and frequent lymphatic metastasis. Therefore, prognostic indicators for ESCC are urgently needed. A-kinase anchor-protein 8-like (AKAP8L) is a member of the A kinase anchor-protein (AKAPs) family and is overexpressed in many cancers. However, the role of AKAP8L in ESCC remains unclear. The aim of this study is to investigate the expression patterns and prognostic value of AKAP8L in ESCC.

Methods
The mRNA expression of AKAP8L was analyzed from the dataset of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Immunohistochemistry was applied to detect the AKAP8L expression in tissue microarray. Pearson’s chi-square test was carried out for the correlation analysis of clinicopathological features and AKAP8L expression. The prognostic significance of clinicopathological features and AKAP8L expression was determined by univariate and multivariate Cox hazard models. Kaplan–Meier survival curve was used for survival analysis.

Results
We found that the mRNA level of AKAP8L was higher in tumor tissues than in adjacent tissues in TCGA and GEO dataset. High AKAP8L expression was associated with poor overall survival (OS) in ESCC patients (p = 0.0039). Besides, AKAP8L expression was highly expressed in patients with lymph node metastasis detected by ESCC tissue microarray (p = 0.0014). The comparison of the different clinicopathological features of ESCC between high and low AKAP8L expression groups revealed that high AKAP8L expression was related to lymph node stage (p = 0.041). Kaplan–Meier survival analysis revealed that high AKAP8L expression indicates an unfavorable progression-free survival (PFS) and OS in ESCC patients (p < 0.0001). Univariate and multivariate analyses confirmed that AKAP8L was an independent prognostic factor for PFS and OS in ESCC (p = 0.003 and p < 0.0001).

Conclusions
In conclusion, this study demonstrated that high expression of AKAP8L is associated with poor prognosis of ESCC and can be considered an independent risk factor for ESCC.
Inferring person-to-person networks of Plasmodium falciparum transmission: are analyses of routine surveillance data up to the task?
Authors: Huber John H. , Hsiang Michelle S. , Dlamini Nomcebo , Murphy Maxwell , Vilakati Sibonakaliso , Nhlabathi Nomcebo , Lerch Anita , Nielsen Rasmus , Ntshalintshali Nyasatu , Greenhouse Bryan , Perkins T. Alex 
Published: February 2022

Abstract
Background
Inference of person-to-person transmission networks using surveillance data is increasingly used to estimate spatiotemporal patterns of pathogen transmission. Several data types can be used to inform transmission network inferences, yet the sensitivity of those inferences to different data types is not routinely evaluated.

Methods
The influence of different combinations of spatial, temporal, and travel-history data on transmission network inferences for Plasmodium falciparum malaria were evaluated.

Results
The information content of these data types may be limited for inferring person-to-person transmission networks and may lead to an overestimate of transmission. Only when outbreaks were temporally focal or travel histories were accurate was the algorithm able to accurately estimate the reproduction number under control, Rc. Applying this approach to data from Eswatini indicated that inferences of Rc and spatiotemporal patterns therein depend upon the choice of data types and assumptions about travel-history data.

Conclusions
These results suggest that transmission network inferences made with routine malaria surveillance data should be interpreted with caution.
Natural history of respiratory muscle strength in spinal muscular atrophy: a prospective national cohort study
Authors: Veldhoen Esther S. , Wijngaarde Camiel A. , Hulzebos Erik H. J. , Wösten-van Asperen Roelie M. , Wadman Renske I. , van Eijk Ruben P. A. , Asselman Fay Lynn , Stam Marloes , Otto Louise A. M. , Cuppen Inge , Scheijmans Feline E. V. , den Oudenrijn Laura P. Verweij-van , Bartels Bart , Gaytant Michael A. , van der Ent Cornelis K. , van der Pol W. Ludo 
Published: February 2022

Abstract
Background
Respiratory complications are the most important cause of morbidity and mortality in spinal muscular atrophy (SMA). Respiratory muscle weakness results in impaired cough, recurrent respiratory tract infections and eventually can cause respiratory failure. We assessed longitudinal patterns of respiratory muscle strength in a national cohort of treatment-naïve children and adults with SMA, hypothesizing a continued decline throughout life.

Methods
We measured maximal expiratory and inspiratory pressure (PEmax and PImax), Sniff Nasal inspiratory pressure (SNIP), peak expiratory flow (PEF), and peak cough flow (PCF) in treatment-naïve patients with SMA. We used mixed-models to analyze natural history patterns.

Results
We included 2172 measurements of respiratory muscle function from 80 treatment-naïve patients with SMA types 1c-3b. All outcomes were lower in the more severe phenotypes. Significant differences in PEF were present between SMA types from early ages onwards. PEF decline was linear (1–2%/year). PEF reached values below 80% during early childhood in types 1c-2, and during adolescence in type 3a. PEmax and PImax were severely lowered in most patients throughout life, with PEmax values abnormally low (i.e. < 80 cmH2O) in virtually all patients. The PEmax/PImax ratio was < 1 throughout life in all SMA types, indicating that expiratory muscles were most affected. All but SMA type 3b patients had a lowered PCF. Patients with types 2b and 3a had PCF levels between 160 and 270 L/min, those with type 2a around 160 L/min and patients with type 1c well below 160 L/min. Finally, SNIP was low in nearly all patients, most pronounced in more severely affected patients.

Conclusions
There are clear differences in respiratory muscle strength and its progressive decline between SMA types. We observed lower outcomes in more severe SMA types. Particularly PEF may be a suitable outcome measure for the follow-up of respiratory strength in patients with SMA. PEF declines in a rather linear pattern in all SMA types, with clear differences at baseline. These natural history data may serve as a reference for longer-term treatment efficacy assessments.
viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data
Authors: Antipov Dmitry , Rayko Mikhail , Kolmogorov Mikhail , Pevzner Pavel A. 
Published: February 2022

AbstractAlthough the use of long-read sequencing improves the contiguity of assembled viral genomes compared to short-read methods, assembling complex viral communities remains an open problem. We describe the viralFlye tool for identification and analysis of metagenome-assembled viruses in long-read assemblies. We show it significantly improves viral assemblies and demonstrate that long-reads result in a much larger array of predicted virus-host associations as compared to short-read assemblies. We demonstrate that the identification of novel CRISPR arrays in bacterial genomes from a newly assembled metagenomic sample provides information for predicting novel hosts for novel viruses.
The efficacy of gabapentin for the treatment of refractory cough associated with interstitial lung disease: study protocol for a randomized, double-blind and placebo-controlled clinical trial
Authors: Gao Ronglin , Xu Xianghuai , Wang Shengyuan , Pu Jincheng , Shi Cuiqin , Wen Siwan , Zhu Yiqing , Tang Jianping , Wang Xuan , Yu Li 
Published: February 2022

Abstract
Introduction
Gabapentin, a neurotransmitter modulator, is thought to treat refractory cough associated with interstitial lung disease by improving cough hypersensitivity.

Methods/design
This is a single-center, prospective, randomized, double-blind, placebo-controlled trial. The trial will investigate the effect of a 10-week course of oral gabapentin 900 mg/day on refractory cough associated with interstitial lung disease (ILD) and explore the possible mechanisms involved in improving cough symptoms. A total of 84 individuals will be randomized in a 1:1 ratio to two treatment groups and will be followed for a total of 14 weeks from the first dose. The primary endpoint of the study will be the change in cough symptom scores at 14 weeks. The secondary endpoints include the change in Leicester Quality of Life Questionnaire (LCQ), Gastroesophageal Reflux Disease Questionnaire (Gerd Q), and Hull Airway Reflux Questionnaire (HARQ) scores; cough sensitivity (C2 and C5) values; and safety.

Discussion
This study will be the first randomized, controlled clinical trial to investigate gabapentin for the treatment of refractory cough associated with interstitial lung disease and provide data on efficacy, safety, and quality of life. If the study confirms that gabapentin is effective in improving refractory cough associated with interstitial lung disease, it will indicate that a deeper understanding of its mechanisms may reveal new therapeutic targets.

Trial registration
Chinese Clinical Trial Registry ChiCTR2100045202. Registered on 8 April 2021, www.chictr.org.cn
Comparison of the procedure time differences between hybrid endoscopic submucosal dissection and conventional endoscopic submucosal dissection in patients with early gastric neoplasms: a study protocol for a multi-center randomized controlled trial (Hybrid-G trial)
Authors: Esaki Mitsuru , Ihara Eikichi , Fujii Hiroyuki , Sumida Yorinobu , Haraguchi Kazuhiro , Takahashi Shunsuke , Iwasa Tsutomu , Nakano Kayoko , Wada Masafumi , Somada Shinichi , Minoda Yosuke , Ogino Haruei , Tagawa Koshiro , Ogawa Yoshihiro 
Published: February 2022

Abstract
Background
Endoscopic submucosal dissection (ESD) is widely accepted as a local treatment for gastrointestinal tract tumors. As a simplified endoscopic procedure, hybrid ESD (H-ESD) has been performed for colorectal neoplasms in recent times. However, whether H-ESD is superior to conventional ESD (C-ESD) for patients with early gastric neoplasms (EGN) remains unclear. In this trial, we will compare the treatment outcomes of H-ESD and C-ESD. We hypothesize that the procedure time for H-ESD is shorter than that for C-ESD.

Methods
This is an investigator-initiated, multi-center, prospective, randomized, open-label, parallel-group trial to be conducted beginning in August 2020 at nine institutions in Japan. We will determine if H-ESD is superior to C-ESD in terms of procedure time in patients with EGN diagnosed as macroscopically intramucosal (T1a) differentiated carcinoma ≤ 20 mm in diameter without ulcerative findings according to current Japanese gastric cancer treatment guidelines. A total of 82 patients will be recruited and randomly assigned to either the C-ESD or the H-ESD group. The primary outcome is ESD procedure time. Secondary outcomes include mucosal incision, time and speed of submucosal dissection, en bloc resection, complete resection, curability, adverse events related to the ESD procedure, extent of dissection before snaring, volume of injection solution, number and time of hemostasis, thickness of the submucosal layer in the resected specimen, and handover to another operator. The stated sample size was determined based on the primary outcome. According to a previous report comparing the procedure times of C-ESD and H-ESD, we hypothesized that H-ESD would provide a 0.2 reduction in logarithmically concerted procedure time (−37%). We estimated that a total of 82 participants were needed to reach a power of 80% for a t-test with a significance level of 0.05 and considering a 10% dropout.

Discussion
This trial will provide high-quality data on the benefits and risks of H-ESD for EGN patients. The results of this study could lead to improved outcomes in patients with EGN undergoing ESD. The results will be presented at national and international meetings and published in peer-reviewed journals.

Trial registration
UMIN-CTR UMIN000041244. Registered on July 29, 2020.
Systematic comparison of published host gene expression signatures for bacterial/viral discrimination
Authors: Bodkin Nicholas , Ross Melissa , McClain Micah T. , Ko Emily R. , Woods Christopher W. , Ginsburg Geoffrey S. , Henao Ricardo , Tsalik Ephraim L. 
Published: February 2022

AbstractBackgroundMeasuring host gene expression is a promising diagnostic strategy to discriminate bacterial and viral infections. Multiple signatures of varying size, complexity, and target populations have been described. However, there is little information to indicate how the performance of various published signatures compare to one another.MethodsThis systematic comparison of host gene expression signatures evaluated the performance of 28 signatures, validating them in 4589 subjects from 51 publicly available datasets. Thirteen COVID-specific datasets with 1416 subjects were included in a separate analysis. Individual signature performance was evaluated using the area under the receiving operating characteristic curve (AUC) value. Overall signature performance was evaluated using median AUCs and accuracies.ResultsSignature performance varied widely, with median AUCs ranging from 0.55 to 0.96 for bacterial classification and 0.69–0.97 for viral classification. Signature size varied (1–398 genes), with smaller signatures generally performing more poorly (P <0.04). Viral infection was easier to diagnose than bacterial infection (84% vs. 79% overall accuracy, respectively;P< .001). Host gene expression classifiers performed more poorly in some pediatric populations (3 months–1 year and 2–11 years) compared to the adult population for both bacterial infection (73% and 70% vs. 82%, respectively;P< .001) and viral infection (80% and 79% vs. 88%, respectively;P< .001). We did not observe classification differences based on illness severity as defined by ICU admission for bacterial or viral infections. The median AUC across all signatures for COVID-19 classification was 0.80 compared to 0.83 for viral classification in the same datasets.ConclusionsIn this systematic comparison of 28 host gene expression signatures, we observed differences based on a signature’s size and characteristics of the validation population, including age and infection type. However, populations used for signature discovery did not impact performance, underscoring the redundancy among many of these signatures. Furthermore, differential performance in specific populations may only be observable through this type of large-scale validation.
Design and implementation of a basic and global point of care ultrasound (POCUS) certification curriculum for emergency medicine faculty
Authors: Russell Frances M. , Kennedy Sarah K. , Rood Loren K. , Nti Benjamin , Herbert Audrey , Rutz Matt A. , Palmer Megan , Ferre Robinson M. 
Published: February 2022

AbstractPoint of care ultrasound (POCUS) use in the emergency department is associated with improved patient outcomes and increased patient satisfaction. When used for procedural guidance, it has been shown to increase first pass success and decrease complications. As of 2012, ultrasound has been identified as a core skill required for graduating emergency medicine (EM) residents. Despite this, only a minority of EM faculty who trained prior to 2008 are credentialed in POCUS. Half of all EM training programs in the United States have less than 50% of their faculty credentialed to perform and teach POCUS to learners. As the use of POCUS continues to grow in medicine, it is especially important to have a pathway for faculty to attain competence and become credentialed in POCUS. The goal of this paper was to outline an implementation process of a curriculum designed to credential EM faculty in POCUS.
Unsupervised IMU-based evaluation of at-home exercise programmes: a feasibility study
Authors: Komaris Dimitrios-Sokratis , Tarfali Georgia , O’Flynn Brendan , Tedesco Salvatore 
Published: February 2022

AbstractBackgroundThe benefits to be obtained from home-based physical therapy programmes are dependent on the proper execution of physiotherapy exercises during unsupervised treatment. Wearable sensors and appropriate movement-related metrics may be used to determine at-home exercise performance and compliance to a physical therapy program.MethodsA total of thirty healthy volunteers (mean age of 31 years) had their movements captured using wearable inertial measurement units (IMUs), after video recordings of five different exercises with varying levels of complexity were demonstrated to them. Participants were then given wearable sensors to enable a second unsupervised data capture at home. Movement performance between the participants’ recordings was assessed with metrics of movement smoothness, intensity, consistency and control.ResultsIn general, subjects executed all exercises similarly when recording at home and as compared with their performance in the lab. However, participants executed all movements faster compared to the physiotherapist’s demonstrations, indicating the need of a wearable system with user feedback that will set the pace of movement.ConclusionIn light of the Covid-19 pandemic and the imperative transition towards remote consultation and tele-rehabilitation, this work aims to promote new tools and methods for the assessment of adherence to home-based physical therapy programmes. The studied IMU-derived features have shown adequate sensitivity to evaluate home-based programmes in an unsupervised manner. Cost-effective wearables, such as the one presented in this study, can support therapeutic exercises that ought to be performed with appropriate speed, intensity, smoothness and range of motion.
Industrial vehicle routing problem: a case study
Authors: Jayarathna D. G. N. D. , Lanel G. H. J. , Juman Z. A. M. S. 
Published: February 2022

AbstractThis study is motivated by a real-world application of ABC (Pvt) Ltd., a well-known FMCG (fast-moving consumer goods) industry. The industry have nine agents (in two operating regions) from which it can serve its 5483 clients. We focus on this industry’s outbound logistics in its two operating regions, namely Colombo and Gampaha, while taking into account its distribution and current decentralized redistribution processes, since additional routing costs have been identified in the existing setup. The goal of this study is to implement a better route plan that optimizes the truck allocation system at the lowest possible costs of transportation, warehouse, and administration. First to determine a best location for the new facility, the gravity model is used to pinpoint the exact location of the central warehouse. Then a centralized delivery strategy is applied to establish a better path between the sub-clusters. The performance of this centralized policy is evaluated on a real-world case study data. The relative cost benefit/saving (34%) of the centralized distribution system is then brought into focus and verified with solid statistics by comparing the overall cost of the centralized distribution system to the total cost of the existing decentralized distribution system. Finally, we highlight how decision-makers and policymakers in the logistics area might use our centralized delivery strategy to reduce extra-costs, particularly during the transportation of commodities.