bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA 3D structure prediction guided by independent folding of homologous sequences
Authors: Magnus Marcin , Kappel Kalli , Das Rhiju , Bujnicki Janusz M. 
Published: October 2019

Abstract

Background
The understanding of the importance of RNA has dramatically changed over recent years. As in the case of proteins, the function of an RNA molecule is encoded in its tertiary structure, which in turn is determined by the molecule’s sequence. The prediction of tertiary structures of complex RNAs is still a challenging task.

Results
Using the observation that RNA sequences from the same RNA family fold into conserved structure, we test herein whether parallel modeling of RNA homologs can improve ab initio RNA structure prediction. EvoClustRNA is a multi-step modeling process, in which homologous sequences for the target sequence are selected using the Rfam database. Subsequently, independent folding simulations using Rosetta FARFAR and SimRNA are carried out. The model of the target sequence is selected based on the most common structural arrangement of the common helical fragments. As a test, on two blind RNA-Puzzles challenges, EvoClustRNA predictions ranked as the first of all submissions for the L-glutamine riboswitch and as the second for the ZMP riboswitch. Moreover, through a benchmark of known structures, we discovered several cases in which particular homologs were unusually amenable to structure recovery in folding simulations compared to the single original target sequence.

Conclusion
This work, for the first time to our knowledge, demonstrates the importance of the selection of the target sequence from an alignment of an RNA family for the success of RNA 3D structure prediction. These observations prompt investigations into a new direction of research for checking 3D structure “foldability” or “predictability” of related RNA sequences to obtain accurate predictions. To support new research in this area, we provide all relevant scripts in a documented and ready-to-use form. By exploring new ideas and identifying limitations of the current RNA 3D structure prediction methods, this work is bringing us closer to the near-native computational RNA 3D models.
The microbiota structure in the cecum of laying hens contributes to dissimilar H2S production
Authors: Huang Chun-Bo , Xiao Lei , Xing Si-Cheng , Chen Jing-Yuan , Yang Yi-Wen , Zhou Yang , Chen Wei , Liang Juan-Boo , Mi Jian-Dui , Wang Yan , Wu Yin-Bao , Liao Xin-Di 
Published: October 2019

Abstract

Background
Host genotype plays a crucial role in microbial composition of laying hens, which may lead to dissimilar odor gas production. The objective of this study was to investigate the relationship among layer breed, microbial structure and odor production.

Results
Thirty Hy-Line Gray and thirty Lohmann Pink laying hens were used in this study to determine the impact of cecal microbial structure on odor production of laying hens. The hens were managed under the same husbandry and dietary regimes. Results of in vivo experiments showed a lower hydrogen sulfide (H2S) production from Hy-Line hens and a lower concentration of soluble sulfide (S2−) but a higher concentration of butyrate in the cecal content of the Hy-Line hens compared to Lohmann Pink hens (P < 0.05), which was consistent with the in vitro experiments (P < 0.05). However, ammonia (NH3) production was not different between genotypes (P > 0.05). Significant microbial structural differences existed between the two breed groups. The relative abundance of some butyrate producers (including Butyricicoccus, Butyricimonas and Roseburia) and sulfate-reducing bacteria (including Mailhella and Lawsonia) were found to be significantly correlated with odor production and were shown to be different in the 16S rRNA and PCR data between two breed groups. Furthermore, some bacterial metabolism pathways associated with energy extraction and carbohydrate utilization (oxidative phosphorylation, pyruvate metabolism, energy metabolism, two component system and secretion system) were overrepresented in the Hy-Line hens, while several amino acid metabolism-associated pathways (amino acid related enzymes, arginine and proline metabolism, and alanine-aspartate and glutamate metabolism) were more prevalent in the Lohmann hens.

Conclusion
The results of this study suggest that genotype of laying hens influence cecal microbiota, which in turn modulates their odor production. Our study provides references for breeding and enteric manipulation for defined microbiota to reduce odor gas emission.
A qualitative transcriptional signature for predicting microsatellite instability status of right-sided Colon Cancer
Authors: Fu Yelin , Qi Lishuang , Guo Wenbing , Jin Liangliang , Song Kai , You Tianyi , Zhang Shuobo , Gu Yunyan , Zhao Wenyuan , Guo Zheng 
Published: October 2019

AbstractBackgroundMicrosatellite instability (MSI) accounts for about 15% of colorectal cancer and is associated with prognosis. Today, MSI is usually detected by polymerase chain reaction amplification of specific microsatellite markers. However, the instability is identified by comparing the length of microsatellite repeats in tumor and normal samples. In this work, we developed a qualitative transcriptional signature to individually predict MSI status for right-sided colon cancer (RCC) based on tumor samples.ResultsUsing RCC samples, based on the relative expression orderings (REOs) of gene pairs, we extracted a signature consisting of 10 gene pairs (10-GPS) to predict MSI status for RCC through a feature selection process. A sample is predicted as MSI when the gene expression orderings of at least 7 gene pairs vote for MSI; otherwise the microsatellite stability (MSS). The classification performance reached the largest F-score in the training dataset. This signature was verified in four independent datasets of RCCs with the F-scores of 1, 0.9630, 0.9412 and 0.8798, respectively. Additionally, the hierarchical clustering analyses and molecular features also supported the correctness of the reclassifications of the MSI status by 10-GPS.ConclusionsThe qualitative transcriptional signature can be used to classify MSI status of RCC samples at the individualized level.
Texture modified diet in German nursing homes: availability, best practices and association with nursing home characteristics
Authors: Burger Carina , Kiesswetter Eva , Alber Rowena , Pfannes Ulrike , Arens-Azevedo Ulrike , Volkert Dorothee 
Published: October 2019

Abstract

Background
For nursing home (NH) residents with swallowing or chewing problems, appealing texture-modified-diets (TMD) need to be available in order to support adequate nutrition. The aim of this study was to describe the availability of TMD and best practices for TMD in German NHs and to identify related NH characteristics.

Methods
Information on NH characteristics, available texture-modified (TM)-levels (soft, “minced & moist”, pureed) and implemented best practices for TMD (derived from menu plan, separately visible components, re-shaped components, considering individual capabilities of the resident) was collected in a survey in German NHs. The number of TM-levels as well as the number of best practices for TMD were tested for their association with 4 structural, 16 operational and 3 resident-related NH characteristics.

Results
The response rate was 7.2% (n = 590) and 563 NHs were included. The vast majority of NHs (95.2%) reported offering “minced & moist” texture and 84.2% preparing separately visible meal components. Several operational characteristics were more frequently (p < 0.05) reported from NHs offering three TM-levels (27.7%) or four best practices for TMD (13.0%) compared to NHs offering one TM-level (28.4%) or one best practice for TMD (20.1%): special diets and delivery forms (e.g. fingerfood 71.2% vs 38.8%; 80.8% vs. 44.3%), written recipes (69.9% vs. 53.1%; 68.5% vs. 53.9%), a dietetic counseling service (85.9% vs. 66.3%; 89.0% vs. 65.2%), a quality circle for nutritional care (66.7% vs. 43.8%; 71.2% vs. 50.4%), regular staff training (89.7% vs. 73.1%; 95.9% vs. 74.8%) and process instructions (73.7% vs. 53.1%; 75.3% vs. 47.8%). No associations were found regarding structural and resident-related NH characteristics, except a higher percentage of residents receiving TMD in NHs with three compared to one TM-level (median 16.3% vs. 13.2%, p = 0.037).

Conclusion
All participating NHs offer some form of TMD, but only a small number offers a selection of TMD and pays adequate attention to its preparation. Operational NH characteristics – which might reflect a general nutritional awareness of the NH – seem to be pivotal for provision of TMD, whereas neither structural nor resident-related characteristics seem to play a role in this regard.
“What would you like to achieve?” Goal-Setting in Patients with Dementia in Geriatric Rehabilitation
Authors: Dutzi Ilona , Schwenk Michael , Kirchner Marietta , Bauer Jürgen M. , Hauer Klaus 
Published: October 2019

Abstract

Background
Setting meaningful, individualized rehabilitation goals is an essential part of the rehabilitation process. Even though patients with dementia are a drastically increasing patient group in geriatric rehabilitation, empirical data about meaningful rehabilitation goals and collaborative goal-setting in this target group is missing. Cognitive impairment and lack of insight in current deficits have been discussed as barriers for participation in goal-setting, but require empirical examination.
This study investigated the feasibility of a semi-structured versus a structured goal-setting approach and the types of goals, rehabilitation patients with mild to moderate dementia perceive as personally relevant. Insights in acute functional and motor deficits, differentiated by cognitive status were explored.

Methods
Cohort study in a geriatric rehabilitation center. Semi-structured and ICF-based, structured interviews were applied to explore patients` rehabilitation goals. Patients` insight in deficits was operationalized as the relationship of self-ratings and objective measures of linked clinical assessments for the same functional construct.

Results
Patients (n = 101, MMSE 22 ± 2.6, age 83.9 ± 5.9 years) stated the improvement of mobility-related functions and self-care activities (> 70%) but also psychological well-being such as handling stress or mood (> 38%) as most important rehabilitation goals. The structured interview facilitated goal-setting and provided a broader view of rehabilitation needs. Correlations between self-ratings and clinical assessments were medium to high (rho = 0.29 to 0.83) with highest associations for key motor features. Trend tests identified a significant trend between values of the clinical assessment and categories of self-ratings (p ≤ 0.01) with lower cognitive status derogating this relationship.

Conclusions
Collaborative goal-setting was feasible, especially when supported by a structured approach and yielded a large spectrum of functional but also psychological rehabilitation needs from the patients` perspective. Patients showed sustained insight in their actual functional impairments, limited in a subgroup of patients with more advanced cognitive impairment.
Pneumonia due to Pandoraea Apista after evacuation of traumatic intracranial hematomas:a case report and literature review
Authors: Lin Chuanzhong , Luo Ning , Xu Qiang , Zhang Jianjun , Cai Mengting , Zheng Guanhao , Yang Ping 
Published: October 2019

Abstract

Background
Pandoraea species is a newly described genus, which is multidrug resistant and difficult to identify. Clinical isolates are mostly cultured from cystic fibrosis (CF) patients. CF is a rare disease in China, which makes Pandoraea a total stranger to Chinese physicians. Pandoraea genus is reported as an emerging pathogen in CF patients in most cases. However, there are few pieces of evidence that confirm Pandoraea can be more virulent in non-CF patients. The pathogenicity of Pandoraea genus is poorly understood, as well as its treatment. The incidence of Pandoraea induced infection in non-CF patients may be underestimated and it’s important to identify and understand these organisms.

Case presentation
We report a 44-years-old man who suffered from pneumonia and died eventually. Before his condition deteriorated, a Gram-negative bacilli was cultured from his sputum and identified as Pandoraea Apista by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS).

Conclusion
Pandoraea spp. is an emerging opportunistic pathogen. The incidences of Pandoraea related infection in non-CF patients may be underestimated due to the difficulty of identification. All strains of Pandoraea show multi-drug resistance and highly variable susceptibility. To better treatment, species-level identification and antibiotic susceptibility test are necessary.
Outbreak of macrolide-resistant mycoplasma pneumoniae in a primary school in Beijing, China in 2018
Authors: Zhang Wen-Zeng , Zhang Song-Jian , Wang Quan-Yi , Li Yin-Dong , Jing Hong-Bo , Hu Guang-Yi , Wu Dan 
Published: October 2019

Abstract

Background
On 7th June, 2018, a primary school in Beijing, China notified Shunyi CDC of an outbreak of acute respiratory disease characterized by fever and cough among students and resulting in nine hospitalization cases during the preceding 2 weeks. We started an investigation to identify the etiologic agent, find additional cases, develop and implement control measures.

Methods
We defined probable cases as students, teachers and other staffs in the school developed fever (T ≥ 37.5 °C) with cough or sore throat; or a diagnosis of pneumonia during May 1–June 31, 2018. Confirmed cases were probable cases with Mycoplasma pneumoniae detected in oropharyngeal (OP) swabs by quantitative real-time polymerase chain reaction (qPCR). We searched case by reviewing school absenteeism records and interviewing students, teachers and staff in this school. Oropharyngeal swabs were collected from symptomatic students. Two qPCR) assay, a duplex qPCR assay, and sequencing were performed to determine the pathogen, genotype and macrolide resistance at the gene level, respectively.

Results
From May 1st to June 31st, 2018, we identified 55 cases (36 probable and 19 confirmed), of whom 25 (45%) were hospitalized for complications. All cases were students, none of the teachers and other staffs in the school were with similar symptoms. The attack rate (AR) was 3.9% (55/1398) for all students. The cases were mainly male (58%), with an age range of 7–8 years (median: 7 years). 72% (18/25) of inpatients had radiograph findings consistent with pneumonia, and some cases were hospitalized for up to 4 weeks. Pathogen detection results indicated that Mycoplasma pneumonia (M. pneumoniae) P1 type 1 was the causative agent in this outbreak, and the strain harbored one point mutation of A to G at position 2063.

Conclusions
The infections by macrolide-resistant M. pneumoniae are not always mild and pneumonia was common and M. pneumoniae could causes serious complications which require long-term hospitalization. In the future infectious disease prevention and control practice, M. pneumoniae should be paid more attention. It is necessary to establish and improve the pathogen and drug resistance surveillance system in order to prevent and control such mutated strains of M. pneumoniae from causing future outbreaks or epidemics in China.
MTHFR and F5 genetic variations have association with preeclampsia in Pakistani patients: a case control study
Authors: Khidri Feriha Fatima , Waryah Yar Muhammad , Ali Faiza Kamran , Shaikh Hina , Ujjan Ikram Din , Waryah Ali Muhammad 
Published: October 2019

AbstractBackgroundTo study the role of single nucleotide variants (SNVs) of genes related to preeclampsia in Pakistani pregnant women.MethodsAfter ethical approval and getting informed consent; 250 pregnant women were enrolled and equally divided into two groups (125 preeclamptic cases and 125 normotensive pregnant women). Demographic details and medical history were recorded, and 10 ml blood sample was obtained for DNA extraction. The tetra-primer amplification refractory mutation system (ARMS) assays were developed for assessing the variants of three preeclampsia related genes;F5,MTHFRandVEGFA. An association of six SNVs;F5:c.1601G > A (rs6025),F5:c.6665A > G (rs6027),MTHFR: c.665C > T (rs1801133),MTHFR: c.1286A > C (rs1801131),VEGFA: c.-2055A > C (rs699947) andVEGFA: c.*237C > T (rs3025039) with preeclampsia was determined by using different genetic models.ResultsGenotyping of the SNVs revealed that patients withMTHFR:c.665C > T, have increased susceptibility to preeclampsia (CT versus CC/TT: OR = 2.79, 95% CI = 1.18–6.59;P* = 0.046 and CT/TT vs CC: OR = 2.91, 95% CI = 1.29–6.57;P* = 0.0497, in overdominant and dominant models, respectively), whereasF5:c.6665A > G, (A/G vs AA/GG: OR = 0.42, 95% CI = 0.21–0.84;P* = 0.038 in overdominant model) andMTHFR:c.1286A > C, (CC versus AA: OR = 0.36, 95% CI = 0.18–0.72;P* = 0.0392 in codominant model) have significantly decreased risk for preeclampsia.F5:c.1601G > A,VEGFA: c.-2055A > CandVEGFA: c.*237C > T variants revealed no relationship with the disease.ConclusionThis is the first case control study describing the protective role ofF5:c.6665A > G against preeclampsia in any world population. In addition, the present study confirmed the association and role ofMTHFRgene variations in the development of preeclampsia in Pakistani patients. Further genetic studies may be required to better understand the complex genetic mechanism of SNVs in preeclampsia related genes in pregnant women.
The association of dialysis adequacy, body mass index, and mortality among hemodialysis patients
Authors: Hong Woong-pyo , Lee Yu-Ji 
Published: October 2019

AbstractBackgroundAlthough hemodialysis (HD) adequacy, single-pool Kt/Vurea(spKt/V), is inversely correlated with body size, each is known to affect patient survival in the same direction. Therefore, we sought to examine the relationship between HD adequacy and mortality according to body mass index (BMI) in HD patients and explore a combination effect of BMI and HD adequacy on mortality risk.MethodsWe retrospectively reviewed patient data from the Korean Society of Nephrology registry, a nationwide database of medical records of HD patients, from January 2001 to June 2017. We included patients ≥18 years old who were receiving maintenance HD. Patients were categorized into three groups according to baseline BMI (< 20 (low), 20 to < 23 (normal), and ≥ 23 (high) kg/m2). Baseline spKt/V was divided into six categories.ResultsAmong 18,242 patients on HD, the median follow-up duration was 5.2 (IQR, 1.9–8.9) years. Cox regression analysis showed that, compared to the reference (spKt/V 1.2–1.4), lower and higher baseline spKt/V were associated with greater and lower risks for all-cause mortality, respectively. However, among patients with high BMI (n = 5588), the association between higher spKt/V and lower all-cause mortality was attenuated in all adjusted models (Pinteraction < 0.001). Compared to patients with normal BMI and spKt/V within the target range (1.2–1.4), those with low BMI had a higher risk for all-cause mortality at all spKt/V levels. However, the gap in mortality risk became narrower for higher values of spKt/V. Compared to patients with normal BMI and spKt/V in the target range, those with high BMI and spKt/V < 1.2 were not at increased risk for mortality despite low dialysis adequacy.ConclusionsThe association between spKt/V and mortality in HD patients may be modified by BMI.
Multiple cerebral metastases and metastatic aneurysms in patients with left atrial Myxoma: a case report
Authors: Wan Yan , Du Hai , Zhang Lei , Guo Shuang , Xu Li , Li Yuanyuan , He Hui , Zhou Lian , Chen Yunping , Mao Ling , Jin Huijuan , Hu Bo 
Published: October 2019

Abstract

Background
Cardiac myxoma is the most common benign cardiac tumor. Brain metastases or multiple cerebral aneurysms are extremely rare, especially for the case of both complications. Brain metastases are usually found at the same time or few months after the diagnosis or surgical removal of cardiac myxoma

Case presentation
We describe a case of patient, operated for a cardiac myxoma, who presented multiple central nervous system metastases associated, cerebral aneurysms and subsequent intracerebral hemorrhage

Conclusions
The long-term follow-up of the patients with atrial myxoma even after complete surgical excision is recommended, especially for the patient with central nervous system manifestations before atrial myxoma excision
Disrespect and abuse during facility-based childbirth in southern Mozambique: a cross-sectional study
Authors: Galle Anna , Manaharlal Helma , Cumbane Emidio , Picardo Joelma , Griffin Sally , Osman Nafissa , Roelens Kristien , Degomme Olivier 
Published: October 2019

Abstract

Background
Evidence suggests that many women experience mistreatment during childbirth in health facilities across the world, but the magnitude of the problem is unknown. The occurrence of disrespect and abuse (D&A) in maternity care services affects the overall quality of care and may undermine women’s trust in the health system. Studies about the occurrence of disrespect and abuse in Mozambican health facilities are scarce. The aim of this study was to explore the experience of women giving birth in hospital in different settings in Maputo City and Province, Mozambique.

Methods
A cross sectional descriptive survey was conducted between April and June 2018 in the Central Hospital of Maputo (HCM) and district hospitals of Manhiça and Marracuene, Maputo Province, Mozambique. Five hundred seventy-two exit interviews were conducted with women leaving the hospital after delivery. The questionnaire consisted of the following components: socio-demographic characteristics, the occurrence of disrespect and abuse, male involvement during labor and childbirth and intrapartum family planning counselling and provision.

Results
Prevalence of disrespect and abuse ranged from 24% in the central hospital to 80% in the district hospitals. The main types of D&A reported were lack of confidentiality/privacy, being left alone, being shouted at/scolded, and being given a treatment without permission. While very few women’s partners attended the births, the majority of women (73-80%) were in favor of involving their partner as a birth companion. Intrapartum counseling of family planning was very low (9-17%).

Conclusion
The occurrence of disrespect and abuse was much higher in the district hospitals compared to the central hospital, emphasizing the high need for interventions outside Maputo City. Allowing male partners as birth companions should be explored further, as women seem in favor of involving their partners. Investing in intrapartum counselling for family planning is currently a missed opportunity for improving the uptake of contraception in the country.