bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements
Authors: Eicher Tara , Chan Jany , Luu Han , Machiraju Raghu , Mathé Ewy A. 
Published: January 2021

AbstractBackgroundAssigning chromatin states genome-wide (e.g. promoters, enhancers, etc.) is commonly performed to improve functional interpretation of these states. However, computational methods to assign chromatin state suffer from the following drawbacks: they typically require data from multiple assays, which may not be practically feasible to obtain, and they depend on peak calling algorithms, which require careful parameterization and often exclude the majority of the genome. To address these drawbacks, we propose a novel learning technique built upon the Self-Organizing Map (SOM), Self-Organizing Map with Variable Neighborhoods (SOM-VN), to learn a set of representative shapes from a single, genome-wide, chromatin accessibility dataset to associate with a chromatin state assignment in which a particular RE is prevalent. These shapes can then be used to assign chromatin state using our workflow.ResultsWe validate the performance of the SOM-VN workflow on 14 different samples of varying quality, namely one assay each of A549 and GM12878 cell lines and two each of H1 and HeLa cell lines, primary B-cells, and brain, heart, and stomach tissue. We show that SOM-VN learns shapes that are (1) non-random, (2) associated with known chromatin states, (3) generalizable across sets of chromosomes, and (4) associated with magnitude and multimodality. We compare the accuracy of SOM-VN chromatin states against the Clustering Aggregation Tool (CAGT), an unsupervised method that learns chromatin accessibility signal shapes but does not associate these shapes with REs, and we show that overall precision and recall is increased when learning shapes using SOM-VN as compared to CAGT. We further compare enhancer state assignments from SOM-VN in signals above a set threshold to enhancer state assignments from Predicting Enhancers from ATAC-seq Data (PEAS), a deep learning method that assigns enhancer chromatin states to peaks. We show that the precision-recall area under the curve for the assignment of enhancer states is comparable to PEAS.ConclusionsOur work shows that the SOM-VN workflow can learn relationships between REs and chromatin accessibility signal shape, which is an important step toward the goal of assigning and comparing enhancer state across multiple experiments and phenotypic states.
Circulating MicroRNA-486 and MicroRNA-146a serve as potential biomarkers of sarcopenia in the older adults
Authors: Liu Huang-Chun , Han Der-Sheng , Hsu Chih-Chin , Wang Jong-Shyan 
Published: January 2021

Abstract
Background
Age-related sarcopenia meaningfully increases the risks of functional limitations and mortality in the older adults. Although circulating microRNAs (c-miRNAs) are associated with aging-related cellular senescence and inflammation, the relationships between c-miRNAs and sarcopenia in the older adults remain unclear. This study investigates whether circulating myo-miRNAs and inflammation-related miRNAs are associated with sarcopenia in the older adults.

Methods
This investigation recruited 77 eligible subjects (41 males and 36 females) from 597 community-dwelling older adults, and then divided them into normal (n = 24), dynapenic (loss of muscular function without mass, n = 35), and sarcopenic groups (loss of muscular function with mass, n = 18). Moreover, myo- (c-miRNA-133a and c-miRNA-486) and inflammation- (c-miRNA-21 and c-miRNA-146a) related miRNAs, as well as, inflammatory-related cytokine and peroxide levels in plasma were determined using quantitative polymerase chain reaction and ELISA, respectively.

Results
Sarcopenic group exhibited lesser skeletal muscle mass index (SMI), handgrip strength, and gait speed, as well as, lower c-miR-486 and c-miR-146a levels, compared to those of normal and dynapenic groups. Moreover, c-miR-486 level was positively related to SMI (r = 0.334, P = 0.003), whereas c-miR-146a level was positively associated with SMI (r = 0.240, P = 0.035) and handgrip strength (r = 0.253, P = 0.027). In the receiver operating characteristic analysis for predicting sarcopenia, the area under the curve in c-miR-486 was 0.708 (95% confidence interval: 0.561–0.855, P = 0.008) and c-miR-146a was 0.676 (95% CI: 0.551–0.801, P = 0.024). However, no significant relationships were observed between SMI/handgrip strength/gait speed and plasma myeloperoxidase/interleukin-1훽/interleukin-6 levels.

Conclusions
Myo-miRNA (c-miR-486) and inflammation-related miRNA (c-miR-146a) are superior to inflammatory peroxide/cytokines in plasma for serving as critical biomarkers of age-related sarcopenia.
Geriatric assessment and intervention in older vulnerable patients undergoing surgery for colorectal cancer: a protocol for a randomised controlled trial (GEPOC trial)
Authors: Dolin Troels G. , Mikkelsen Marta , Jakobsen Henrik L. , Nordentoft Tyge , Pedersen Trine S. , Vinther Anders , Zerahn Bo , Vistisen Kirsten K. , Suetta Charlotte , Nielsen Dorte , Johansen Julia S. , Lund Cecilia M. 
Published: January 2021

Abstract
Background
The incidence of colorectal cancer (CRC) increases with age. Older patients are a heterogeneous group ranging from fit to frail with various comorbidities. Frail older patients with CRC are at increased risk of negative outcomes and functional decline after cancer surgery compared to younger and fit older patients. Maintenance of independence after treatment is rarely investigated in clinical trials despite older patients value it as high as survival. Comprehensive geriatric assessment (CGA) is an evaluation of an older persons’ medical, psychosocial, and functional capabilities to develop an overall plan for treatment and follow-up. The beneficial effect of CGA is well documented in the fields of medicine and orthopaedic surgery, but evidence is lacking in cancer surgery. We aim to investigate the effect of CGA on physical performance in older frail patients undergoing surgery for CRC.

Methods
GEPOC is a single centre randomised controlled trial including older patients (≥65 years) undergoing surgical resection for primary CRC. Frail patients (≤14/17 points using the G8 screening tool) will be randomised 1:1 to geriatric intervention and exercise (n = 50) or standard of care along (n = 50) with their standard surgical procedure. Intervention includes preoperative CGA, perioperative geriatric in-ward review and postoperative follow-up. All patients in the intervention group will participate in a pre- and postoperative resistance exercise programme (twice/week, 2 + 12 weeks). Primary endpoint is change in 30-s chair stand test. Assessment of primary endpoint will be performed by physiotherapists blinded to patient allocation. Secondary endpoints: changes in health related quality of life, physical strength and capacity (handgrip strength, gait speed and 6 min walking test), patient perceived quality of recovery, complications to surgery, body composition (Dual-energy X-ray absorptiometry and bioelectric impedance), serum biomarkers, readmission, length of stay and survival.

Discussion
This ongoing trial will provide valuable knowledge on whether preoperative CGA and postoperative geriatric follow-up and intervention including an exercise program can counteract physical decline and improve quality of life in frail CRC patients undergoing surgery.

Trial registration
Prospectively registered at Clinicaltrials.gov NCT03719573 (October 2018).
Self-rated health among people living with HIV in Spain in 2019: a cross-sectional study
Authors:   on behalf of the Hospital Survey Study Group, Ruiz-Algueró Marta , Hernando Victoria , Marcos Henar , Gutiérrez Gonzalo , Pérez-Elías Maria Jesus , López-Bernaldo de Quirós Juan Carlos , Pulido Federico , Górgolas Miguel , Sanz Jesus , Suarez-García Ines , Fernandez Maria Teresa , Losa Juan Emilio , Pérez Jose Luis , Ladrero Maria Oliva , Prieto Miguel Ángel , González Gustavo , Izquierdo Ana , Viloria Luis Javier , López Irene , Martínez Eva , Castrillejo Daniel , Aranguren Rosa , Belmonte Maria Antonia , Aranda-García I V , Arraiza Antonio , Diaz Asuncion 
Published: January 2021

Abstract
Background
HIV infection has become a chronic disease and well-being of people living with HIV (PLHIV) is now of particular concern. The objectives of this paper were to describe self-rated health among PLHIV, on ART and on ART virally suppressed and to analyse its determinants.

Methods
Data were obtained from a second-generation surveillance system based on a cross-sectional one-day survey in public hospitals. Epidemiological and clinical data were collected among HIV-infected inpatients and outpatients receiving HIV-related care the day of the survey in 86 hospitals in 2019. Self-rated health was measured using a question included in the National Health Survey: “In the last 12 months, how would you rate your health status?” an ordinal variable with five categories (very good, good, moderate, bad and very bad). For the analysis, these responses were dichotomized into two categories: 1 = very good/good and 0 = moderate, bad or very bad health status. Factors associated with very good/good self-rated health were estimated using logistic regression.

Results
Of 800 PLHIV, 67.5% perceived their health as very good/good, 68.4% among PLHIV on ART and 71.7% of those virally suppressed. Having university education (adjusted odds ratio (aOR):2.1), being unemployed (aOR:0.3) or retired (aOR:0.2), ever being diagnosed of AIDS (aOR:0.6), comorbidities (aOR:0.3), less than 2 year since HIV diagnosis (aOR:0.3) and not receiving ART (aOR:0.3) were associated with good self-rated health. Moreover, among PLHIV on ART, viral load less than 200 copies (aOR:3.2) were related to better perceived health. Bad adherence was inversely associated with good self-rated health among PLHIV on ART (aOR:0.5) and of those virally suppressed (aOR:0.4).

Conclusions
Nearly seven in 10 PLHIV in Spain considered their health status as very good/good, being higher among virally suppressed PLHIV. Both demographic and clinical determinants affect quality of life.
Seroprevalence of hepatitis c virus infection among blood donors in Ethiopia: a systematic review and meta-analysis
Authors: Lake Eyasu Alem , Fite Robera Olana , Gebrekirstos Lielt Gebreselassie , Gebremedhin Meron Hadis , Obsa Mohammed Suleiman , Gelaw Kelemu Abebe 
Published: January 2021

Abstract
Background
Blood transfusion is one of the routine therapeutic interventions in hospitals that can be lifesaving. However, this intervention is related to several transfusion-related infections. Hepatitis C viral infection is one of the most common causes of transfusion-related hepatitis. Subsequently, this systematic review and meta-analysis was aimed to estimate the seroprevalence of hepatitis C virus infection among blood donors in Ethiopia.

Methods
PubMed, Google Scholar, Health InterNetwork Access to Research Initiative (HINARI), Excerpta Medica database (EMBASE), and Cochrane library, the web of science, African journal of online (AJOL), and Google Scholar was searched. The data were extracted using Microsoft Excel and analyzed by using STATA version 14. Publication bias was checked by funnel plot, contour-enhanced funnel plots, trim and fill analysis and more objectively through Egger’s regression test, with P <  0.05 considered to indicate potential publication bias. The heterogeneity of studies was checked using I2 statistics. Pooled analysis was conducted using a weighted inverse variance random-effects model. Subgroup analysis was done by region and study period. A sensitivity analysis was employed.

Result
A total of 25 studies with 197,172 study participants were used to estimate the seroprevalence of hepatitis c virus among blood donors. The overall seroprevalence of hepatitis C virus was 0.819% (95% CI: 0.67–0.969; I2 = 92.3%). Regional sub-group analysis showed that the pooled prevalence of hepatitis c virus infection among blood donors found to be 0.563% in Somali, 1.08% in Oromia, 0.847% in Amhara, and 0.908% in south nations nationalities and peoples region.

Conclusion
The pooled seroprevalence of hepatitis C virus infection among blood donors in Ethiopia found to be low. Moreover, there should be systematic strategies that enhance donor screening and retention of safe regular donors.
The influence of the CRS-R score on functional outcome in patients with severe brain injury receiving early rehabilitation
Authors: Boltzmann Melanie , Schmidt Simone B. , Gutenbrunner Christoph , Krauss Joachim K. , Stangel Martin , Höglinger Günter U. , Wallesch Claus-W. , Rollnik Jens D. 
Published: January 2021

AbstractBackgroundThe aim of the study was to determine the role of the Coma Recovery Scale-Revised (CRS-R) in the prediction of functional status at the end of neurological early rehabilitative treatment.MethodsPatients consecutively admitted to intensive or intermediate care units of a neurological rehabilitation center were enrolled in the study. Consciousness and functional status were assessed with the Coma Recovery Scale-Revised (CRS-R) and the Early Rehabilitation Barthel Index (ERBI), respectively. Both assessments were carried out weekly within the first month and at the end of early rehabilitation. Patient and clinical data were entered into a binary logistic regression model to predict functional status at discharge.Results327 patients (112 females, 215 males) with a median age of 63 years (IQR = 53–75) and a median disease duration of 18 days (IQR = 12–28) were included. Most patients suffered from stroke (59 %), followed by traumatic brain injury (31 %), and hypoxic ischemic encephalopathy (10 %). Upon admission, 12 % were diagnosed as comatose, 31 % as unresponsive wakefulness syndrome (UWS), 35 % as minimally conscious state (MCS) and 22 % already emerged from MCS (eMCS). Of all patients undergoing complete early rehabilitative treatment (n = 180), 72 % showed improvements in level of consciousness (LOC). In this group, age, initial CRS-R score and gains in CRS-R score after four weeks independently predicted functional outcome at discharge.ConclusionsThe study confirms the relevance of the CRS-R score for functional outcome prediction. High CRS-R scores and young age facilitate functional improvements and increase the probability to continue treatment in subsequent rehabilitation phases. Moreover, results indicate that recovery might occur over a period of time that extends beyond acute care.
Real-world assessment of the impact of “OFF” episodes on health-related quality of life among patients with Parkinson’s disease in the United States
Authors: Thach Andrew , Jones Eddie , Pappert Eric , Pike James , Wright Jack , Gillespie Alexander 
Published: January 2021

Abstract
Background
Many patients with Parkinson’s disease (PD) who receive carbidopa/levodopa experience symptom reemergence or worsening, or “OFF” episodes. This study assessed the association of “OFF” episodes with health-related quality of life (HRQoL).

Methods
US-specific data from the 2017 and 2019 Adelphi Real World Disease Specific Programme for PD, a real-world cross-sectional survey, were used. Neurologists provided data for 10–12 consecutive patients with PD who completed the 39-item Parkinson’s Disease Questionnaire (PDQ-39) and the EuroQol 5-Dimension (EQ-5D). Data were grouped by patients who experienced “OFF” episodes versus those who did not and by average hours of daily “OFF” time. Differences between patient groups were assessed for demographics and clinical characteristics; regression analyses were used to model the relationship between HRQoL and “OFF” episodes with age, sex, body mass index, current PD stage on the Hoehn and Yahr scale, and number of concomitant conditions related and unrelated to mobility as covariates.

Results
Data from 722 patients were analyzed. Overall, 321 patients (44%) had “OFF” episodes (mean of 2.9 h of daily “OFF” time). Patients who experienced “OFF” episodes were less likely to work full-time and more likely to live with family members other than their spouse/partner or reside in a long-term care facility than those without “OFF” episodes. The presence of “OFF” episodes, regardless of the average hours of daily “OFF” time, was significantly associated with high scores (reflecting poor HRQoL) on most PDQ-39 dimensions and the summary index and low scores (reflecting poor health status) on the EQ-5D health utility index, visual analog scale (VAS), and all dimensions. Furthermore, increased average hours of daily “OFF” time was significantly correlated with higher scores for all PDQ-39 dimensions and the summary index, as well as with the EQ-5D health utility index and VAS scores. Patients with “OFF” episodes experienced reduced HRQoL even after correcting for potentially confounding variables.

Conclusions
This study demonstrated that the occurrence of “OFF” episodes in patients with PD is associated with reduced HRQoL and that the impact on HRQoL increased incrementally with increasing average hours of daily “OFF” time.
Association of placental chorangiosis with pregnancy complication and prenatal outcome: a case-control study
Authors: Vafaei Homeira , Karimi Zinat , Akbarzadeh-Jahromi Mojgan , Asadian Fatemeh 
Published: January 2021

AbstractBackgroundChorangiosis is a vascular change involving the terminal chorionic villi in the placenta. It results from longstanding, low-grade hypoxia in the placental tissue, and is associated with such conditions as intrauterine growth restriction (IUGR), diabetes, and gestational hypertension in pregnancy. Chorangiosis rarely occurs in normal pregnancies. However, its prevalence is 5–7% of all placentas from infants admitted to newborn intensive care units. The present study was aimed at determining the association of chorangiosis with pregnancy complications and perinatal outcomes.MethodsIn this case-control study, 308 chorangiosis cases were compared with 308 controls (with other diagnoses in pathology) in terms of maternal, placental, prenatal, and neonatal characteristics derived from the medical records of participants retrospectively. R and SPSS version 22 software tools were used, and the statistical significance level was considered 0.05 for all the tests.ResultsPreeclampsia, diabetes mellitus, maternal hemoglobin, maternal hematocrit, C/S, oligohydramnios, fetal anomaly, dead neonates, NICU admissions were significantly higher in the chorangiosis group OR = 1.6, 3.98, 1.68, 1.92, 2.1, 4.47, 4.22, 2.9, 2.46, respectively (p-value< 0.05 for all). Amniotic fluid index, birth weight, cord PH amount, 1st, and 5th Apgar score was lower in the chorangiosis group OR = 0.31, 1, 0.097, 0.83, 0.85, respectively (p-value< 0.05 for all). Moreover, fundal placenta, retro placental hemorrhage, perivillous fibrin deposition, calcification, and acute chorioamnionitis were higher in the chorangiosis group OR = 2.1, 11.8, 19.96, 4.05, and 6.38 respectively, (p-value< 0.05). There was a high agreement between the two pathologists, and the power of the study was estimated at 99%.ConclusionAlthough chorangiosis is an uncommon condition, it is associated with a higher incidence of perinatal and neonatal morbidity and mortality. Therefore, it should be considered an important clinical sign of adverse pregnancy outcomes and should be reported in the pathology evaluation.
“Mine did not breastfeed”, mothers’ experiences in breastfeeding children aged 0 to 24 months with oral clefts in Uganda
Authors: Nabatanzi Maureen , Seruwagi Gloria Kimuli , Tushemerirwe Florence Basiimwa , Atuyambe Lynn , Lubogo David 
Published: January 2021

Abstract
Background
Appropriate breastfeeding is vital for infant and young child nutrition. Annually, oral clefts affect 0.73 per 1000 children in Uganda. Despite this low incidence, children with a cleft face breastfeeding difficulty which affect their nutrition status. In addition, knowledge on maternal experiences with breastfeeding and support is limited. We explored maternal perceptions, experiences with breastfeeding and support received for their children 0 to 24 months with a cleft attending Comprehensive Rehabilitative Services of Uganda (CoRSU) Hospital.

Methods
This cross-sectional study combined quantitative and qualitative methods. We consecutively recruited 32 mothers of children with a cleft aged 0 to 24 months attending CoRSU hospital between April and May 2018. A structured questionnaire collected data on breastfeeding practices and device use (n = 32). To gain a broad understanding of mothers’ perceptions and experiences with breastfeeding and support received, we conducted two Focus Group Discussions (in each, n = 5), and 15 In Depth Interviews. Descriptive statistics were analyzed using SPSS software. Qualitative data were analyzed thematically.

Results
Of the 32 children with a cleft, 23(72%) had ever breastfed, 14(44%) were currently breastfeeding, and among those under 6 months, 7(35%) exclusively breastfed. Of 25 mothers interviewed in IDIs and FGDs, 17(68%; IDIs = 8/15, FGD1 = 5/5 and FGD2 = 4/5) reported the child’s failure to latch and suckle as barriers to breastfeeding. All ten mothers who used the soft squeezable bottle reported improved feeding. Nineteen (76%) mothers experienced anxiety and 14(56%), social stigma. Family members, communities and hospitals supported mothers with feeding guidance, money, child’s feeds and psycho-social counselling. Appropriate feeding and psycho-social support were only available at a specialized hospital which delayed access.

Conclusions
Breastfeeding practices were sub-optimal. Mothers experienced breastfeeding difficulties, anxiety and social stigma. Although delayed, feeding, social and psycho-social support helped mothers cope. Routine health care for mothers and their children with a cleft should include timely support.
Monozygotic twins discordant for homologous Robertsonian translocation trisomy 21 of 46, XX, + 21, der (21;21) (q10; q10) in a twin-to-twin transfusion syndrome, case report
Authors: Cao Dingya , Sun Jimei , Li Nan , Li Zhihua , Liu Weiqiang , Chen Min 
Published: January 2021

AbstractBackgroundMonozygotic twins are nearly identical in genotype and phenotype because monozygotic twins arise from one fertilized oocyte. In all cases of discordant karyotype in monozygotic twins, trisomy 21 accounts for about one in 385,000. Monozygotic twins discordant for Robertsonian translocation trisomy 21 of the der (21;21)(q10;q10), in which the additional chromosome originates from the father is rare.Case presentationA 28-year-old parous woman, G3P1A0, came to our institution for a dating scan at 8 weeks of gestation. The transvaginal ultrasound examination demonstrated a monochorionic diamniotic pregnancy. She and her husband were healthy, with no family history of trisomy 21 or other congenital diseases. The ultrasound examination of nuchal translucency thickness was discordant in twins at 13 weeks (twin A, NT 1.4 mm with CRL being 65 mm; twin B, NT 7.8 mm with CRL being 69 mm). At 17+ 4weeks, twin A was normal, but ventricular septal defect and the hypoplastic left heart was detected in twin B. The deepest vertical pocket was 18 mm in twin A (oligohydramnios) and 102 mm in Twin B (polyhydramnios). The bladder in twin A was absent. Ultrasound findings indicated TTTS Stage II. Amniocentesis was performed for the two fetuses. The karyotyping results revealed 46, XX in twin A but 46,XX,+ 21,der (21;21)(q10;q10) in twin B.For twin B, the parents opted for selective fetal termination by radiofrequency ablation. The procedure was uneventful. At 40+ 5weeks, twin A was born with a birth weight of 4120 g by vaginal delivery.ConclusionsThe early detection of discordant karyotype and twin-to-twin transfusion syndrome is beneficial to the early intervention. In monozygotic twins with a discordant anomaly, the discordant karyotype should be considered.