bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of pathogens from native urine samples by MALDI-TOF/TOF tandem mass spectrometry
Authors: Oros Damir , Ceprnja Marina , Zucko Jurica , Cindric Mario , Hozic Amela , Skrlin Jasenka , Barisic Karmela , Melvan Ena , Uroic Ksenija , Kos Blazenka , Starcevic Antonio 
Published: June 2020

Abstract
Background
Reliable high-throughput microbial pathogen identification in human urine samples is crucial for patients with cystitis symptoms. Currently employed methods are time-consuming and could lead to unnecessary or inadequate antibiotic treatment. Purpose of this study was to assess the potential of mass spectrometry for uropathogen identification from a native urine sample.

Methods
In total, 16 urine samples having more than 105 CFU/mL were collected from clinical outpatients. These samples were analysed using standard urine culture methods, followed by 16S rRNA gene sequencing serving as control and here described culture-independent MALDI-TOF/TOF MS method being tested.

Results
Here we present advantages and disadvantages of bottom-up proteomics, using MALDI-TOF/TOF tandem mass spectrometry, for culture-independent identification of uropathogens (e.g. directly from urine samples). The direct approach provided reliable identification of bacteria at the genus level in monobacterial samples. Taxonomic identifications obtained by proteomics were compared both to standard urine culture test used in clinics and genomic test based on 16S rRNA sequencing.

Conclusions
Our findings indicate that mass spectrometry has great potential as a reliable high-throughput tool for microbial pathogen identification in human urine samples. In this case, the MALDI-TOF/TOF, was used as an analytical tool for the determination of bacteria in urine samples, and the results obtained emphasize high importance of storage conditions and sample preparation method impacting reliability of MS2 data analysis. The proposed method is simple enough to be utilized in existing clinical settings and is highly suitable for suspected single organism infectious etiologies. Further research is required in order to identify pathogens in polymicrobial urine samples.
Impact of sub-setting the data of the main Limousin beef cattle population on the estimates of across-country genetic correlations
Authors: Bonifazi Renzo , Vandenplas Jeremie , Napel Jan ten , Matilainen Kaarina , Veerkamp Roel F. , Calus Mario P. L. 
Published: June 2020

AbstractBackgroundCattle international genetic evaluations allow the comparison of estimated breeding values (EBV) across different environments, i.e. countries. For international evaluations, across-country genetic correlations (rg) need to be estimated. However, lack of convergence of the estimated parameters and high standard errors of thergare often experienced for beef cattle populations due to limited across-country genetic connections. Furthermore, using all available genetic connections to estimatergis prohibitive due to computational constraints, thus sub-setting the data is necessary. Our objective was to investigate and compare the impact of strategies of data sub-setting on estimated across-countryrgand their computational requirements.MethodsPhenotype and pedigree information for age-adjusted weaning weight was available for ten European countries and 3,128,338 Limousin beef cattle males and females. Using a Monte Carlo based expectation–maximization restricted maximum likelihood (MC EM REML) methodology, we estimated across-countryrgby using a multi-trait animal model where countries are modelled as different correlated traits. Values ofrgwere estimated using the full data and four different sub-setting strategies that aimed at selecting the most connected herds from the largest population.ResultsUsing all available data, direct and maternalrg(standard errors in parentheses) were on average equal to 0.79 (0.14) and 0.71 (0.19), respectively. Direct-maternal within-country and between-countryrgwere on average equal to − 0.12 (0.09) and 0.00 (0.14), respectively. Data sub-setting scenarios gave similar results: on average, estimatedrgwere smaller compared to using all data for direct (0.02) and maternal (0.05) genetic effects. The largest differences were obtained for the direct-maternal within-country and between-countryrg, which were, on average 0.13 and 0.12 smaller compared to values obtained by using all data. Standard errors always increased when reducing the data, by 0.02 to 0.06, on average. The proposed sub-setting strategies reduced the required computing time up to 22% compared to using all data.ConclusionsEstimating all 120 across-countryrgthat are required for beef cattle international evaluations, using a multi-trait MC EM REML approach, is feasible but involves long computing time. We propose four strategies to reduce computational requirements while keeping a multi-trait estimation approach. In all scenarios with data sub-setting, the estimatedrgwere consistently smaller (mainly for direct-maternalrg) and had larger standard errors.
Association of functional limitations and disability with elder abuse in India: a cross-sectional study
Authors: Sathya T. , Premkumar Ramaswamy 
Published: June 2020

AbstractBackgroundGlobally, elder abuse is a common form of violence against the elderly. This study examines the association of disability and functional ability measures with elder abuse in India.MethodsCross-sectional data from the UNFPA’s ‘Building Knowledge Base on Population Ageing in India’ (BKPAI 2011) have been analysed. Bivariate and multivariate logistic regression analyses have been used to examine the association of measures of disability and functional ability with elder abuse/mistreatment.ResultsThe overall prevalence of elder abuse in the study population is 11.4%. The prevalence of elder abuse experienced by study participants in the month before the survey is 6%. The prevalence of disability/functional ability increases the likelihood of elder abuse. Furthermore, the association between functional ability and abuse is stronger and consistent among the elderly who experienced abuse in the month preceding the survey. In addition, the association between disability and elder abuse is stronger in urban areas. Another observation is that gender introduces considerable disparities in the association of disability and functional ability measures with elder abuse. While elderly men with more than two disabilities are 1.85 times (95% CI: 1.23, 2.77,p < 0.003) more likely to experience abuse/mistreatment, women are 3.16 times (CI: 2.22, 4.49,p < .001) more exposed to it.ConclusionsThe results of this study suggest a significant association of disability and functional ability with elder abuse. The association differs considerably by place of residence and gender. Measures to improve the functional health of the elderly population and measures to protect the elderly with disability and functional limitations are important in preventing abuse/mistreatment in old age.
Risk factors for disease progression in COVID-19 patients
Authors: Chang Min Cheol , Park Yu-Kyung , Kim Bong-Ok , Park Donghwi 
Published: June 2020

Abstract
Background
Coronavirus disease (COVID-19) is rapidly spreading worldwide. Although 10–20% of patients with COVID-19 have severe symptoms, little is known about the risk factors related to the aggravation of COVID-19 symptoms from asymptomatic or mild to severe disease states.

Methods
This retrospective study included 211 patients who were asymptomatic or with mild presentations of COVID-19. We evaluated the differences in demographic and clinical data between the cured (discharged to home) and transferred (aggravated to severe-stage COVID-19) groups.

Results
A multivariate logistic analysis showed that body temperature, chills, initial chest X-ray findings, and the presence of diabetes were significantly associated with predicting the progression to severe stage of COVID-19 (p < 0.05). The odds ratio of transfer in patients with COVID-19 increased by 12.7-fold for abnormal findings such as haziness or consolidation in initial chest X-ray, 6.32-fold for initial symptom of chills, and 64.1-fold for diabetes.

Conclusions
Even if patients are asymptomatic or have mild symptoms, clinicians should closely observe patients with COVID-19 presenting with chills, body temperature > 37.5 °C, findings of pneumonia in chest X-ray, or diabetes.
Multilevel ordinal model for CD4 count trends in seroconversion among South Africa women
Authors: Dessie Zelalem G. , Zewotir Temesgen , Mwambi Henry , North Delia 
Published: June 2020

Abstract
Background
Ordinal health longitudinal response variables have distributions that make them unsuitable for many popular statistical models that assume normality. We present a multilevel growth model that may be more suitable for medical ordinal longitudinal outcomes than are statistical models that assume normality and continuous measurements.

Methods
The data is from an ongoing prospective cohort study conducted amongst adult women who are HIV-infected patients in Kwazulu-Natal, South Africa. Participants were enrolled into the acute infection, then into early infection subsequently into established infection and afterward on cART. Generalized linear multilevel models were applied.

Results
Multilevel ordinal non-proportional and proportional-odds growth models were presented and compared. We observed that the effects of covariates can’t be assumed identical across the three cumulative logits. Our analyses also revealed that the rate of change of immune recovery of patients increased as the follow-up time increases. Patients with stable sexual partners, middle-aged, cART initiation, and higher educational levels were more likely to have better immunological stages with time. Similarly, patients having high electrolytes component scores, higher red blood cell indices scores, higher physical health scores, higher psychological well-being scores, a higher level of independence scores, and lower viral load more likely to have better immunological stages through the follow-up time.

Conclusion
It can be concluded that the multilevel non-proportional-odds method provides a flexible modeling alternative when the proportional-odds assumption of equal effects of the predictor variables at every stage of the response variable is violated. Having higher clinical parameter scores, higher QoL scores, higher educational levels, and stable sexual partners were found to be the significant factors for trends of CD4 count recovery.
CT findings of patients infected with SARS-CoV-2
Authors: Wang Xiaoyang , Liu Chenbin , Hong Liang , Yuan Cuiyun , Ding Jiguang , Jia Qing , Sun Gangqiang , Peng Wenxian , Sun Qingfeng 
Published: June 2020

AbstractBackgroundWe aimed to describe the chest CT findings in sixty-seven patients infected by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).MethodsWe retrospectively reviewed 67 patients hospitalized in Ruian People’s Hospital. All the patients received the positive diagnosis of SARS-CoV-2 infection. The CT and clinical data were collected between January 23rd, 2020 and February 10th, 2020. The CT images were analyzed by the senior radiologists.ResultsThere are 54 patients with positive CT findings and 13 patients with negative CT findings. The typical CT findings in hospitalized patients with SARS-CoV-2 infection were ground glass opacities (42/54), lesions located in the peripheral area (50/54), multiple lesions (46/54), and lesions located in the lower lobes (42/54). There were less typical CT findings, including air bronchogram (18/54), pleural thickening or pleural effusion (14/54), consolidation (12/54), lesions in the upper lobes (12/54), interlobular septal thickening (11/54), reversed halo sign (9/54), single lesion (8/54), air cavities (4/54), bronchial wall thickening (3/54), and intrathoracic lymph node enlargement (2/54).ConclusionsCT features can play an important role in the early diagnosis and follow-up of COVID-19 patients.
Treatment of recurrent renal transplant lithiasis: analysis of our experience and review of the relevant literature
Authors: Li Xiaohang , Li Baifeng , Meng Yiman , Yang Lei , Wu Gang , Jing Hongwei , Bi Jianbin , Zhang Jialin 
Published: June 2020

Abstract
Background
Renal transplant lithiasis is a rather unusual disease, and the recurrence of lithiasis presents a challenging situation.

Methods
We retrospectively analyzed the medical history of one patient who suffered renal transplant lithiasis twice, reviewed the relevant literature, and summarized the characteristics of this disease.

Results
We retrieved 29 relevant studies with an incidence of 0.34 to 3.26% for renal transplant lithiasis. The summarized incidence was 0.52%, and the recurrence rate was 0.082%. The mean interval after transplantation was 33.43 ± 56.70 mo. Most of the patients (28.90%) were asymptomatic. The management included percutaneous nephrolithotripsy (PCNL, 22.10%), ureteroscope (URS, 22.65%), extracorporeal shockwave lithotripsy (ESWL, 18.60%) and conservative treatment (17.13%). In our case, the patient suffered from renal transplant lithiasis at 6 years posttransplantation, and the lithiasis recurred 16 months later. He presented oliguria, infection or acute renal failure (ARF) during the two attacks but without pain. PCNL along with URS and holmium laser lithotripsy were performed. The patient recovered well after surgery, except for a 3 mm residual stone in the calyx after the second surgery. He had normal renal function without any symptoms and was discharged with oral anticalculus drugs and strict follow-up at the clinic. Fortunately, the calculus passed spontaneously about 1 month later.

Conclusions
Due to the lack of specific symptoms in the early stage, patients with renal transplant lithiasis may have delayed diagnosis and present ARF. Minimally invasive treatment is optimal, and the combined usage of two or more procedures is beneficial for patients. After surgery, taking anticalculus drugs, correcting metabolic disorders and avoiding UIT are key measures to prevent the recurrence of lithiasis.
Ex vivo modelling of drug efficacy in a rare metastatic urachal carcinoma
Authors: Mäkelä Rami , Arjonen Antti , Härmä Ville , Rintanen Nina , Paasonen Lauri , Paprotka Tobias , Rönsch Kerstin , Kuopio Teijo , Kononen Juha , Rantala Juha K. 
Published: June 2020

Abstract
Background
Ex vivo drug screening refers to the out-of-body assessment of drug efficacy in patient derived vital tumor cells. The purpose of these methods is to enable functional testing of patient specific efficacy of anti-cancer therapeutics and personalized treatment strategies. Such approaches could prove powerful especially in context of rare cancers for which demonstration of novel therapies is difficult due to the low numbers of patients. Here, we report comparison of different ex vivo drug screening methods in a metastatic urachal adenocarcinoma, a rare and aggressive non-urothelial bladder malignancy that arises from the remnant embryologic urachus in adults.

Methods
To compare the feasibility and results obtained with alternative ex vivo drug screening techniques, we used three different approaches; enzymatic cell viability assay of 2D cell cultures and image-based cytometry of 2D and 3D cell cultures in parallel. Vital tumor cells isolated from a biopsy obtained in context of a surgical debulking procedure were used for screening of 1160 drugs with the aim to evaluate patterns of efficacy in the urachal cancer cells.

Results
Dose response data from the enzymatic cell viability assay and the image-based assay of 2D cell cultures showed the best consistency. With 3D cell culture conditions, the proliferation rate of the tumor cells was slower and potency of several drugs was reduced even following growth rate normalization of the responses. MEK, mTOR, and MET inhibitors were identified as the most cytotoxic targeted drugs. Secondary validation analyses confirmed the efficacy of these drugs also with the new human urachal adenocarcinoma cell line (MISB18) established from the patient’s tumor.

Conclusions
All the tested ex vivo drug screening methods captured the patient’s tumor cells’ sensitivity to drugs that could be associated with the oncogenic KRASG12V mutation found in the patient’s tumor cells. Specific drug classes however resulted in differential dose response profiles dependent on the used cell culture method indicating that the choice of assay could bias results from ex vivo drug screening assays for selected drug classes.
Utilization of machine learning to test the impact of cognitive processing and emotion recognition on the development of PTSD following trauma exposure
Authors: Augsburger Mareike , Galatzer-Levy Isaac R. 
Published: June 2020

Abstract
Background
Though lifetime exposure to traumatic events is significant, only a minority of individuals develops symptoms of posttraumatic stress disorder (PTSD). Post-trauma alterations in neurocognitive and affective functioning are likely to reflect changes in underlying brain networks that are predictive of PTSD. These constructs are assumed to interact in a highly complex way. The aim of this exploratory study was to apply machine learning models to investigate the contribution of these interactions on PTSD symptom development and identify measures indicative of circuit related dysfunction.

Methods
N = 94 participants admitted to the emergency room of an inner-city hospital after trauma exposure completed a battery of neurocognitive and emotional tests 1 month after the incident. Different machine learning algorithms were applied to predict PTSD symptom severity and clusters after 3 months based.

Results
Overall, model accuracy did not differ between PTSD clusters, though the importance of cognitive and emotional domains demonstrated both key differences and overlap. Alterations in higher-order executive functioning, speed of information processing, and processing of emotionally incongruent cues were the most important predictors.

Conclusions
Data-driven approaches are a powerful tool to investigate complex interactions and can enhance the mechanistic understanding of PTSD. The study identifies important relationships between cognitive processing and emotion recognition that may be valuable to predict and understand mechanisms of risk and resilience responses to trauma prospectively.
Low uptake of continuous subcutaneous insulin infusion therapy in people with type 1 diabetes in Ireland: a retrospective cross-sectional study
Authors: Gajewska Katarzyna Anna , Bennett Kathleen , Biesma Regien , Sreenan Seamus 
Published: June 2020

Abstract
Background
The uptake of continuous subcutaneous insulin infusion (CSII) therapy in those with type 1 diabetes varies internationally and is mainly determined by the national healthcare reimbursement systems. The aim of this study is to estimate national and regional uptake of CSII therapy in children, adolescents and adults with type 1 diabetes in Ireland.

Methods
A retrospective cross-sectional study was conducted utilizing the national pharmacy claims database in 2016. Individuals using CSII were identified by dispensing of infusion sets. The uptake of CSII was calculated as the percentage of people with type 1 diabetes claiming CSII sets in 2016, both in children and adolescent (age < 18 years) and adult populations (≥ 18 years). Descriptive statistics including percentages with 95% confidence intervals (CIs) are presented, stratified by age-groups and geographical regions, and chi-square tests used for comparisons.

Results
Of 20,081 people with type 1 diabetes, 2111 (10.5, 95% CI: 10.1–10.9%) were using CSII in 2016. Uptake was five-fold higher in children and adolescents at 34.7% (95% CI: 32.9–36.5%) than in adults at 6.8% (95% CI: 6.4–7.2%). Significant geographical heterogeneity in CSII uptake was found, from 12.6 to 53.7% in children and adolescents (p < 0.001), and 2 to 9.6% in adults (p < 0.001).

Conclusions
Uptake of CSII in people with type 1 diabetes is low in Ireland, particularly in those ≥18 years. Identification of barriers to uptake, particularly in this group, is required.
A rare long-term undetected pheochromocytoma leading to Takotsubo syndrome in an older male patient: a case report
Authors: Chen Min , Zhao Tong , Chen Guoping , Hu Shenjiang 
Published: June 2020

AbstractBackgroundTakotsubo syndrome is an uncommon, acute, and reversible cardiomyopathy that occurs primarily in postmenopausal females. The clinical presentation of the syndrome resembles acute coronary syndrome, but coronary angiography reveals no obstructive coronary artery disease. Rarely, a catecholamine surge due to pheochromocytoma may induce Takotsubo syndrome. The clinical features of pheochromocytoma include paroxysmal hypertension, headache, palpitations, and profuse sweating. However, owing to the episodic, rather than continued, symptoms and signs of pheochromocytoma, its timely diagnosis poses a challenge for clinicians. Here, we report a rare case of long-term undetected pheochromocytoma leading to Takotsubo syndrome in an older male patient.Case presentationA 70-year-old man presented with paroxysmal chest distress and chest pain. Examinations revealed acute coronary syndrome with normal coronary arteries, heart failure, reversible left ventricular regional wall motion abnormalities, labile blood pressure, a giant left adrenal mass, and extremely high levels of metanephrine and normetanephrine. Clinical manifestations, laboratory reports, and imaging findings suggested a diagnosis of Takotsubo syndrome caused by pheochromocytoma. Supportive therapy, administration of alpha- adrenergic receptor blockers, and left adrenal mass resection resolved the patient’s symptoms. A histological examination confirmed the presence of pheochromocytoma. We reviewed his history of midbrain hemorrhage 6 years prior and found a mass in the left adrenal region by reviewing the computed tomography images of the lung that were also taken 6 years prior, on which the pheochromocytoma was evident.ConclusionsOur case illustrates the importance of understanding the link between pheochromocytoma and Takotsubo syndrome. A diagnosis of pheochromocytoma-induced Takotsubo syndrome should be considered during the differential diagnosis of acute coronary syndrome, especially in patients with labile blood pressure and normal coronary angiography findings; meanwhile, assessments of catecholamines and its metabolites and abdominal computed tomography scan should be performed at the right time. Clinicians should also be alert to potential pheochromocytoma in patients with unexplained cerebral hemorrhage, even in the absence of symptoms of catecholamine excess.