bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional decline in geriatric rehabilitation ward; is it ascribable to Hospital Acquired Infection? A prospective cohort study.
Authors: Laurent Marie , Oubaya Nadia , David Jean Philippe , Poitrine Florence Canoui , Corsin Lola , Liuu Evelyne , Audureau Etienne , Garin Sylvie Bastuji , Paillaud Elena 
Published: March 2020

Abstract
Background: Some patients may not benefit from their stay in a geriatric rehabilitation unit and paradoxically worsened their functional status. The incidence of functional decline in these units and factors associated with this decline have not been clearly identified. Methods: We used a prospective cohort of consecutive patients aged ≥ 75 years admitted to a geriatric rehabilitation unit in a French university hospital. The main endpoint was functional decline defined by at least an one-point decrease in Activities of Daily Living (ADL) score during the stay. Baseline social and geriatric characteristics were recorded and comorbidities were sought by the Cumulative Illness Rating Scale for Geriatrics (CIRS-G). During follow-up, hospital-acquired infection (HAI) was recorded, as was ADL score at discharge. Multivariate logistic regression and mediation analyses were used to identify factors associated with ADL decrease. Results : Among the 252 eligible patients, 165 (median age 85 years [interquartile range (IQR) 81-90] had available ADL scores at baseline (median score 7 [IQR 4-10]) and at discharge (median 9 [6-12]). Median CIRS-G score was 11 [9-13], 24 (14.5%) had a pulmonary HAI; 30 (18.2%) showed functional decline. On multivariable analysis, functional decline was associated with comorbidities (global CIRS-G score, P=0.02, CIRS-G for respiratory disease [CIRS-G-R] ≥2, P=0.03, or psychiatric disease, P=0.02) and albumin level < 35 g/l (p=0.02). Significant association were found between functional decline and CIRS-G for respiratory diseases (CIRS-G-R) (OR 2.82 [95% CI 1.18-6.71], p=0.016), between functional decline and pulmonary HAI (OR 4.09 [1.48-11.34],p=4.09), and between CIRS-G-R and pulmonary HAI (OR 10.9 [5.26-22.5],p=0.0001). Theses associations and the reduced effect of CIRS-G-R on functional decline after adjusting for pulmonary HAI (OR 1.91 [0.71-5.16], p=0.20) suggested partial mediation of pulmonary HAI in the relation between CIRS-G-R and functional decline. Conclusion : Baseline comorbidities were independently associated with functional decline in patients hospitalized in a geriatric rehabilitation unit. Pulmonary HAI may have mediated this association. We need to better identify patients at risk of functional decline before transfer to a rehabilitation unit and to test the implementation of modern and individual programs of rehabilitation outside the hospital for these patients.
Bomb Blast: Imaging Findings, Treatment and Clinical Course of Extremity Traumas
Authors: Tahtabasi Mehmet , Er Sadettin , Karasu Recep , Ucaroglu Erhan Renan 
Published: March 2020

Abstract
Background: To determine the severity and types of blast-related extremity injuries and the presence of accompanying vascular injuries (VI) and amputation, and to identify the predictive factors affecting the treatment management and clinical course.Methods: The study included 101 patients with extremity injuries caused by a bomb explosion. The radiographs and computed tomography angiographies of the patients were evaluated in terms of injury patterns, presence of shrapnel fragments and fractures, and localization (upper or lower extremity) and type (open or closed) of injury. In addition, the presence of soft tissue injuries and VI was recorded. The Gustilo-Anderson classification was used for open fractures. According to their severity, open fractures classified as types 1, 2 and 3A were included in Group 1 and those classified as type 3B and 3C in Group 2.Results: As a result of the explosion, 101 (57.7%) patients had extremity injuries, of which 76 (75.2%) presented with at least one fracture. Of the total of 103 fractures, nine (8.8%) were closed and 94 (91.2%) were open. Thirty-eight (40.4%) of the open fractures were located in the upper extremities, and 56 (59.6%) in the lower extremities and pelvis. Open fractures were most frequently localized in the femur (n=20; 21.2%), followed by the tibia (n=18; 19.1%). The majority of patients with open fractures were in Group 1 (74.2%). The duration of hospital stay was longer in Group 2 (11.7±5.8 vs. 6.8±6.7 days, p <0.0001). Mortality among patients in Group 2 (44.4%) was significantly higher than in Group 1 (6.1%) ( p <0.0001). Similarly, the injury severity score (ISS) was higher in Group 2 (median 20 vs. 9, p<0.0001). Similarly, the rate of VI was higher in Group 2 (66.1%) than in Group 1 (2.4%) ( p <0.0001). VI was present in 13 (12.9%) of all patients, and amputation in seven (7.9%). The most common localization of amputation was transtibial (n=3).Conclusion: The presence of severe open fractures, VI, and high ISS score can be considered as important factors that increase morbidity and mortality. In extremity traumas, through the secondary blast mechanism, contaminated-fragmented tissue injuries occur. Therefore, we believe that it will be beneficial to apply damage control surgery in places with low socioeconomic level and poor hygienic conditions.
Genome wide association studies for japonica rice resistance to blast in field and controlled conditions
Authors: Volante Andrea , Tondelli Alessandro , Desiderio Francesca , Abbruscato Pamela , Menin Barbara , Biselli Chiara , Casella Laura , Singh Namrata , McCouch Susan R. , Tharreau Didier , Zampieri Elisa , Cattivelli Luigi , Valè Giampiero 
Published: March 2020

Abstract
Background Rice blast, caused by the fungus Pyricularia oryzae , represents the most damaging fungal disease of rice worldwide. Utilization of resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different blast strains. Results The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs no obvious candidates or positional relationships were identified, raising the possibility that these loci harbor previously unidentified blast resistance genes. ConclusionsWe identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.
Qualitative analysis of clinicians’ perspectives on the use of a computerized decision aid in the treatment of psychotic disorders
Authors: Roebroek Lukas , Bruins Jojanneke , Delespaul Philippe A. , Boonstra Albert , Castelein Stynke 
Published: March 2020

Abstract
Background: Clinical decision aids are used in various medical fields to support patients and clinicians when making healthcare decisions. Few attempts have been made to implement such tools in psychiatry. We developed Treatment E-Assist (TREAT); a routine outcome monitoring based computerized clinical decision aid, which generates personalized treatment recommendations in the care of people with psychotic disorders. The aim of this study is to investigate how TREAT is used and evaluated by clinicians and how this tool can be improved.Methods: Clinicians working with TREAT during a clinical trial were asked to participate in semi-structured interviews. The unified theory of acceptance and use of technology (UTAUT) was adopted to structure the interview questions. The transcripts were coded. An inductive thematic analysis was followed to identify the main themes.Results: 13 clinicians (mean age: 49) of which eight psychiatrists and five nurse practitioners, participated in this study. Eight clinicians experienced TREAT as beneficial, whereas five experienced no additional benefits. Thematic analysis revealed five themes about how TREAT was used and evaluated by clinicians, views on TREAT’s visual structuring of routine outcome monitoring results, guideline based treatment recommendations, contextual factors, effects on patients and effects on shared decision-making. Performance and effort expectancy were perceived as high by clinicians. The facilitating conditions were optimal and perceived social influence was low.Conclusion: This article presents a qualitative evaluation by clinicians of a computerized clinical decision aid in psychosis care. TREAT was viewed by most clinicians as beneficial during their consultations. The visual representation of routine outcome monitoring results was well-appreciated and provided input to discuss treatment planning with patients. The treatment recommendations did not change most treatment decisions but supported clinical reasoning. However, some clinicians were unconvinced about TREAT’s benefits. The delivery, applicability and the availability of resources require improvement to increase TREAT’s efficacy. Not all patients responded well to TREAT but the observed facilitation of shared decision-making is promising. All four predictors of the unified theory of acceptance and use of technology were positively evaluated by the majority of clinicians. Clinicians behavioral intentions are expected to be high when implementing TREAT into organizations.
Signs and symptoms do not predict, but may help rule out acute Q fever in favour of other respiratory tract infections, and reduce antibiotics overuse in primary care
Authors: Hackert Volker Heinz , Dukers-Muijrers Nicole H.T.M. , Hoebe Christian J.P.A. 
Published: March 2020

Abstract
Background From early 2009, South Limburg, Netherlands, experienced a massive outbreak of Q fever, overlapping with the influenza A(H1N1)pdm09 pandemic during the second half of the year and affecting approximately 2.9% of the regional population. Acute Q fever shares clinical features with other respiratory conditions. Most symptomatic acute infections are characterized by mild symptoms, or an isolated febrile syndrome. Pneumonia was present in a majority of hospitalized patients during the Dutch 2007-2010 Q fever epidemic. Early empiric doxycycline, guided by signs and symptoms and patient history, should not be delayed awaiting laboratory confirmation, as it may shorten disease and prevent progression to focalized persistent Q fever. We assessed signs’ and symptoms’ association with acute Q fever to guide early empiric treatment in primary care patients. Methods In response to the outbreak, regional primary care and hospital-based specialty physicians tested a total of 1228 subjects for Q fever. Testing activity was bimodal, a first “wave” lasting from March to December 2009, followed by a second “wave” which lasted into 2010 and coincided with peak pandemic influenza activity. We approached all 253 notified acute Q fever cases and a random sample of 457 Q fever negative individuals for signs and symptoms of disease. Using data from 140/229(61.1%) Q fever positive and 194/391(49.6%) Q fever negative respondents from wave 1, we built symptom-based models predictive of Q-fever outcome, validated against each other and against our wave 2 data. Results Our models had moderate AUC scores (0.68% to 0.72%), with low positive (4.6-8.3%), but high negative predictive values (91.7-99.5%). Male sex, fever, and pneumonia were strong positive predictors, while cough was a strong negative predictor of acute Q fever in these models. Conclusion Whereas signs and symptoms of disease do not appear to predict acute Q fever, they may help rule it out in favour of other respiratory conditions, prompting a delayed or non-prescribing approach instead of early empiric doxycycline in primary care patients with non-severe presentations. Signs and symptoms thus may help reduce the overuse of antibiotics in primary care during and following outbreaks of Q fever.
Expression of FAM83H and ZNF16 are associated with shorter survival of patients with gallbladder carcinoma
Authors: Ahn Sung Woo , Ahn Ae-Ri , Ha Sang Hoon , Hussein Usama Khamis , Yang Jae Do , Kim Kyoung Min , Park Ho Sung , Park See-Hyoung , Yu Hee Chul , Jang Kyu Yun 
Published: March 2020

Abstract
BackgroundRecently, FAM83H was reported to have roles in cancer progression in conjunction with oncogenic molecules such as MYC and b-catenin. Moreover, the data from the public database indicates a molecular relationship between FAM83H and zinc finger proteins, especially between FAM83H and ZNF16. However, studies on FAM83H and ZNF16 in gallbladder cancer have been limited. MethodsThis study investigated the expression of FAM83H and ZNF16 in 105 gallbladder carcinomas. ResultsIn human gallbladder carcinomas, immunohistochemical expression of FAM83H was significantly associated with ZNF16 expression. In univariate analysis, nuclear and cytoplasmic expression of FAM83H or ZNF16 were significantly associated with shorter survival of gallbladder carcinoma patients. Multivariate analysis revealed the nuclear expression of FAM83H as an independent indicator of poor prognosis of overall survival (p = 0.005) and relapse-free survival (p = 0.005) of gallbladder carcinoma patients. Moreover, co-expression patterns of nuclear FAM83H and ZNF16 were also independent indicators of shorter survival of gallbladder carcinoma patients (overall survival; p < 0.001, relapse-free survival; p < 0.001). ConclusionsThis study suggests FAM83H and ZNF16 are associated with the progression of gallbladder carcinoma, and the expressions of FAM83H and ZNF16 might be novel prognostic indicators of gallbladder carcinoma patients.
Interaction Between HIF-1α and Notch Signaling Pathways in Nucleus Pulposus Cells of Patients with Modic Changes
Authors: Xiong Zekang , Guo Xiaodong , Zheng Jin , Ding Jun , Zhou Jinge , Yao Sheng 
Published: March 2020

Abstract
Background The HIF-1α/Notch signaling pathway has been shown to regulate proliferation, apoptosis, and metabolism in the intervertebral disc (IVD). The NP is an important structure adjacent to the disc. However, the roles of HIF1α and Notch signaling pathways in NP cells of patients with different Modic changes (MCs) are unclear. The purpose of this research was to assess the expression and association of HIF-1α and components of the Notch pathway in nucleus pulposus (NP) tissue of patients with various MCs. Methods Eighty-five surgical NP tissue samples were obtained from patients undergoing microdiscectomy procedures for the treatment of low back and root pain caused by prolapse of the IVD. The NP tissues were divided into four groups based on the adjacent endplate degeneration: MC I, II, III, and negative MC groups. The expression of HIF-1α and Notch-related components were measured and compared. Results The expression of HIF-1α, Notch1, and Notch2 were gradually increased in the MC I and MC II groups compared with that of the negative MC group. Meanwhile, HIF-1α and Notch-related components were rarely detected in MC III group. Conclusions The expression of HIF-1α/Notch is increased in the NP cells of patients with MC I and MC II. Application of the association between HIF-1α/Notch signaling pathway could be promising target for clinical diagnosis and treatment of disc degeneration in MC patients.
Complications of bone transport technique using the Ilizarov method in the lower extremity: a retrospective analysis of 282 consecutive cases over 10 years
Authors: Liu Yanshi , Yushan Maimaiaili , Liu Zhenhui , Liu Jialin , Ma Chuang , Ahemaitijiang Yusufu 
Published: March 2020

Abstract
Background: The treatment of large bone defects in lower limbs is a serious challenge for orthopedic surgeons and patients. The bone transport technique according to the Ilizarov method characterized with versatile abilities and has become the main option for the reconstruction of bone defect. However, inevitable difficulties as complications related to bone transport technique have been reported by many studies. Complications which could affect on the clinical outcomes remain a major concern. The purpose of this study was to evaluate the effectiveness and complications of bone transport technique using Ilizarov method in the treatment of bone defect in lower extremity.Methods: The study was conducted on 282 patients who underwent bone transport procedures using Ilizarov method at our institution from January 2007 to June 2017. Patient’s demographic data, complications and clinical outcomes at two years follow-up were collected and retrospectively analyzed. All difficulties that related to bone transport were documented according to Paley’s classification. The clinical outcomes were evaluated using Association for the Study and Application of the Method of Ilizarov criteria (ASAMI) at last clinical visit.Results: There were 243 male and 39 females with a mean age of 40 years (range 18-65 years). The mean defect was 6.56±2.15 cm, whereas single level transport in 221 cases and double level transport in 61 cases. A total of 189 problems, 166 obstacles and 406 complications (257 minor and 149 major complications) were observed，the average complication rate per patients consists of 0.91 minor and 0.53 major complications. The top five complications were pin-site infection (65.96%), axial deviation (40.78%), joint stiffness (23.76%), soft tissue incarceration (22.34%) and delayed union of the docking site (13.48%).The ASAMI bony result was excellent in 233 patients, good in 32, fair in 5 and poor in 12. The ASAMI functional result was excellent in 136 patients, good in 88, fair in 47, poor in 11 and failure in 0.Conclusion: Bone transport is a reliable method for reconstruction of bone defects in the femur and tibia caused by variety of reasons. Particular attention, patient’s compliance and experience of the surgeon contribute the satisfactory results.
Aveolar Macrophage Activation and Cytokine Storm in the Pathogenesis of Severe COVID-19
Authors: Wang Chaofu , Xie Jing , Zhao Lei , Fei Xiaochun , Zhang Heng , Tan Yun , Zhou Luting , Liu Zhenhua , Ren Yong , Yuan Ling , Zhang Yu , Zhang Jinsheng , Liang Liwei , Chen Xinwei , Liu Xin , Wang Peng , Han Xiao , Weng Xiangqin , Chen Ying , Yu Ting , Zhang Xinxin , Cai Jun , Chen Rong , Shi Zhengli , Bian Xiuwu 
Published: March 2020

Abstract
The coronavirus disease-19 (COVID-19) caused by SARS-CoV-2 infection can lead to a series of clinical settings from non-symptomatic viral carriers/spreaders to severe illness characterized by acute respiratory distress syndrome (ARDS)1,2. A sizable part of patients with COVID-19 have mild clinical symptoms at the early stage of infection, but the disease progression may become quite rapid in the later stage with ARDS as the common manifestation and followed by critical multiple organ failure, causing a high mortality rate of 7-10% in the elderly population with underlying chronic disease1-3. The pathological investigation in the lungs and other organs of fatal cases is fundamental for the mechanistic understanding of severe COVID-19 and the development of specific therapy in these cases. Gross anatomy and molecular markers allowed us to identify, in two fatal patients subject to necropsy, the main pathological features such as exudation and hemorrhage, epithelium injuries, infiltration of macrophages and fibrosis in the lungs. The mucous plug with fibrinous exudate in the alveoli and the activation of alveolar macrophages were characteristic abnormalities. These findings shed new insights into the pathogenesis of COVID-19 and justify the use of interleukin 6 (IL6) receptor antagonists and convalescent plasma with neutralizing antibodies against SARS-CoV-2 for severe patients.Authors Chaofu Wang, Jing Xie, Lei Zhao, Xiaochun Fei, Heng Zhang, and Yun Tan contributed equally to this work. Authors Chaofu Wang, Jun Cai, Rong Chen, Zhengli Shi, and Xiuwu Bian jointly supervised this work.
Tumor Response Prediction in 90Y Radioembolization with PET-based Radiomics Features and Absorbed Dose Metrics
Authors: Wei Lise , Cui Can , Xu Jiarui , Kaza Ravi , Naqa Issam El , Dewaraja Yuni K 
Published: March 2020

Abstract
Purpose Evaluate whether lesion radiomics features and absorbed dose metrics extracted from post-therapy 90 Y PET can be integrated to better predict outcome in microsphere radioembolization of liver malignancies. Methods Given the noisy nature of 90 Y PET, first, a liver phantom study with repeated acquisitions and varying reconstruction parameters was used to identify a subset of robust radiomics features for the patient analysis. In 36 radioembolization procedures, 90 Y PET/CT was performed within a couple of hours to extract 46 radiomics features and estimate absorbed dose in 105 primary and metastatic liver lesions. Robust radiomics modeling was based on bootstrapped multivariate logistic regression with shrinkage regularization (LASSO) and Cox regression with LASSO. Nested cross-validation and bootstrap resampling were used for optimal parameter/feature selection and for guarding against overfitting risks. Spearman rank correlation was used to analyze feature associations. Area under the receiver-operating characteristics curve (AUC) was used for lesion response (at first follow-up) analysis while Kaplan-Meier plots and c-index were used to assess progression model performance. Models with absorbed dose only, radiomics only and combined models were developed to predict lesion outcome. Results The phantom study identified 15/46 reproducible and robust radiomics features that were subsequently used in the patient models. A lesion response model with zone percentage (ZP) and mean absorbed dose achieved an AUC of 0.729 (95%CI: 0.702-0.758) and a progression model with zone size nonuniformity (ZSN) and absorbed dose achieved a c-index of 0.803 (95% CI: 0.790-0.815) on nested cross validation (CV). The combined models outperformed the radiomics only and absorbed dose only models. Conclusion We have developed new lesion-level response and progression models using textural radiomics features, derived from 90 Y PET combined with mean absorbed dose for predicting outcome in radioembolization. These encouraging results may need further validation in independent datasets prior to clinical adoption.