bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using neighborhood cohesiveness to infer interactions between protein domains
Authors: Segura Joan , Sorzano C. O. S. , Cuenca-Alba Jesus , Aloy Patrick , Carazo J. M. 
Published: April 2015

Abstract
Motivation: In recent years, large-scale studies have been undertaken to describe, at least partially, protein-protein interaction maps, or interactomes, for a number of relevant organisms, including human. However, current interactomes provide a somehow limited picture of the molecular details involving protein interactions, mostly because essential experimental information, especially structural data, is lacking. Indeed, the gap between structural and interactomics information is enlarging and thus, for most interactions, key experimental information is missing. We elaborate on the observation that many interactions between proteins involve a pair of their constituent domains and, thus, the knowledge of how protein domains interact adds very significant information to any interactomic analysis.
Results: In this work, we describe a novel use of the neighborhood cohesiveness property to infer interactions between protein domains given a protein interaction network. We have shown that some clustering coefficients can be extended to measure a degree of cohesiveness between two sets of nodes within a network. Specifically, we used the meet/min coefficient to measure the proportion of interacting nodes between two sets of nodes and the fraction of common neighbors. This approach extends previous works where homolog coefficients were first defined around network nodes and later around edges. The proposed approach substantially increases both the number of predicted domain-domain interactions as well as its accuracy as compared with current methods.
Availability and implementation: http://dimero.cnb.csic.es
Contact: jsegura@cnb.csic.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Synergistic and singular effects of river discharge and lunar illumination on dam passage of upstream migrant yellow-phase American eels
Authors: Welsh Stuart A. , Aldinger Joni L. , Braham Melissa A. , Zimmerman Jennifer L. 
Published: April 2015

Abstract
Monitoring of dam passage can be useful for management and conservation assessments of American eel, particularly if passage counts can be examined over multiple years. During a 7-year study (2007–2013) of upstream migration of American eels within the lower Shenandoah River (Potomac River drainage), we counted and measured American eels at the Millville Dam eel pass, where annual study periods were determined by the timing of the eel pass installation during spring or summer and removal during fall. Daily American eel counts were analysed with negative binomial regression models, with and without a year (YR) effect, and with the following time-varying environmental covariates: river discharge of the Shenandoah River at Millville (RDM) and of the Potomac River at Point of Rocks, lunar illumination (LI), water temperature, and cloud cover. A total of 17 161 yellow-phase American eels used the pass during the seven annual periods, and length measurements were obtained from 9213 individuals (mean = 294 mm TL, s.e. = 0.49, range 183–594 mm). Data on passage counts of American eels supported an additive-effects model (YR + LI + RDM) where parameter estimates were positive for river discharge (β = 7.3, s.e. = 0.01) and negative for LI (β = −1.9, s.e. = 0.34). Interestingly, RDM and LI acted synergistically and singularly as correlates of upstream migration of American eels, but the highest daily counts and multiple-day passage events were associated with increased RDM. Annual installation of the eel pass during late spring or summer prevented an early spring assessment, a period with higher RDM relative to those values obtained during sampling periods. Because increases in river discharge are climatically controlled events, upstream migration events of American eels within the Potomac River drainage are likely linked to the influence of climate variability on flow regime.
Description of IMP-31, a novel metallo-β-lactamase found in an ST235 Pseudomonas aeruginosa strain in Western Germany
Authors: Pfennigwerth Niels , Geis Gabriele , Gatermann Sören G. , Kaase Martin 
Published: April 2015

Abstract

Objectives
The objective of this study was to characterize a novel IMP-type metallo-β-lactamase (MBL) found in an MDR clinical isolate of Pseudomonas aeruginosa.

Methods
The P. aeruginosa isolate NRZ-00156 was recovered from an inguinal swab from a patient hospitalized in Western Germany and showed high MICs of carbapenems. MBL production was analysed by Etest for MBLs, an EDTA combined disc test and an EDTA bioassay. Typing of the isolate was performed by MLST. Genetic characterization of the new blaIMP gene was performed by sequencing the PCR products. A phylogenetic tree was constructed. The novel blaIMP gene was expressed in Escherichia coli TOP10 and the enzyme was subjected to biochemical characterization.

Results
The P. aeruginosa isolate NRZ-00156 expressed the ST235 allelic profile and was resistant to all the β-lactams tested except aztreonam. The isolate was positive for MBL production and harboured a new IMP allele, blaIMP-31, located on a disrupted class I integron [also carrying the blaOXA-35, aac(6′)-Ib, aac(3)-Ic and aphA15 genes]. Its closest relative was IMP-35, with 96.7% amino acid identity. Expression of blaIMP-31 demonstrated that E. coli TOP10 producing IMP-31 had elevated resistance to all the β-lactams tested except aztreonam. Kinetic data were obtained for both IMP-31 and IMP-1. In comparison with IMP-1, IMP-31 showed weaker hydrolytic activity against all the β-lactams tested, which resulted from lower kcat values.

Conclusions
The characterization of the new IMP-type gene blaIMP-31 from an ST235 P. aeruginosa isolate indicates an ongoing spread of highly divergent IMP-type carbapenemases in clinical P. aeruginosa strains and highlights the continuous need for the prevention of nosocomial infections caused by MDR Gram-negative bacteria.
Next-generation sequencing reveals the biological significance of the N
2,3-ethenoguanine lesion in vivo
Authors: Chang Shiou-chi , Fedeles Bogdan I. , Wu Jie , Delaney James C. , Li Deyu , Zhao Linlin , Christov Plamen P. , Yau Emily , Singh Vipender , Jost Marco , Drennan Catherine L. , Marnett Lawrence J. , Rizzo Carmelo J. , Levine Stuart S. , Guengerich F. Peter , Essigmann John M. 
Published: April 2015

Abstract
Etheno DNA adducts are a prevalent type of DNA damage caused by vinyl chloride (VC) exposure and oxidative stress. Etheno adducts are mutagenic and may contribute to the initiation of several pathologies; thus, elucidating the pathways by which they induce cellular transformation is critical. Although N 2,3-ethenoguanine (N 2,3-εG) is the most abundant etheno adduct, its biological consequences have not been well characterized in cells due to its labile glycosidic bond. Here, a stabilized 2′-fluoro-2′-deoxyribose analog of N 2,3-εG was used to quantify directly its genotoxicity and mutagenicity. A multiplex method involving next-generation sequencing enabled a large-scale in vivo analysis, in which both N 2,3-εG and its isomer 1,N 2-ethenoguanine (1,N 2-εG) were evaluated in various repair and replication backgrounds. We found that N 2,3-εG potently induces G to A transitions, the same mutation previously observed in VC-associated tumors. By contrast, 1,N 2-εG induces various substitutions and frameshifts. We also found that N 2,3-εG is the only etheno lesion that cannot be repaired by AlkB, which partially explains its persistence. Both εG lesions are strong replication blocks and DinB, a translesion polymerase, facilitates the mutagenic bypass of both lesions. Collectively, our results indicate that N 2,3-εG is a biologically important lesion and may have a functional role in VC-induced or inflammation-driven carcinogenesis.
The Prevalence and Associated Distress of Physical and Psychological Symptoms in Patients With Advanced Heart Failure Attending a South African Medical Center
Authors: Lokker Martine E. , Gwyther Liz , Riley Jillian P. , van Zuylen Lia , van der Heide Agnes , Harding Richard 
Published: April 2015

Background:
Despite the high prevalence of heart failure in low- and middle-income countries, evidence concerning patient-reported burden of disease in advanced heart failure is lacking.

Objective:
The aim of this study is to measure patient-reported symptom prevalence and correlates of symptom burden in patients with advanced heart failure.

Methods:
Adult patients diagnosed with New York heart Association (NYHA) stage III or IV heart failure were recruited from the emergency unit, emergency ward, cardiology ward, general medicine wards, and outpatient cardiology clinic of a public hospital in South Africa. Patients were interviewed by researchers using the Memorial Symptom Assessment Scale–Short Form, a well-validated multidimensional instrument that assesses presence and distress of 32 symptoms.

Results:
A total of 230 patients (response, 99.1%), 90% NYHA III and 10% NYHA IV (12% newly diagnosed), with a mean age of 58 years, were included. Forty-five percent were women, 14% had completed high school, and 26% reported having no income. Mean Karnofsky Performance Status Score was 50%. Patients reported a mean of 19 symptoms. Physical symptoms with a high prevalence were shortness of breath (95.2%), feeling drowsy/tired (93.0%), and pain (91.3%). Psychological symptoms with a high prevalence were worrying (94.3%), feeling irritable (93.5%), and feeling sad (93.0%). Multivariate linear regression analyses, with total number of symptoms as dependent variable, showed no association between number of symptoms and gender, education, number of healthcare contacts in the last 3 months, years since diagnosis, or comorbidities. Increased number of symptoms was significantly associated with higher age (b = 0.054, P = .042), no income (b = −2.457, P = .013), and fewer hospitalizations in the last 12 months (b = −1.032, P = .017).

Conclusions:
Patients with advanced heart failure attending a medical center in South Africa experience high prevalence of symptoms and report high levels of burden associated with these symptoms. Improved compliance with national and global treatment recommendations could contribute to reduced symptom burden. Healthcare professionals should consider incorporating palliative care into the care for these patients.
Effects of Amoxicillin and Clavulanic Acid on the Spontaneous Mechanical Activity of Juvenile Rat Duodenum
Authors: Ciciora Steven L. , Williams Kent C. , Gariepy Cheryl E. 
Published: April 2015

AbstractObjectives:There are a limited number of medications for the treatment of foregut dysmotility. Enteral amoxicillin/clavulanic acid induces phase III duodenal contractions in a fasting pediatric patient. The mechanism by which this occurs is unknown. We examined the individual contributions of amoxicillin and clavulanic acid on the spontaneous mechanical activity of juvenile rat duodenum to better understand this phenomenon.Methods:Duodenal segments from juvenile rats were longitudinally attached to force transducers in organ baths. Samples were cumulatively exposed to amoxicillin or clavulanic acid. Separate samples were exposed to carbachol alone to assess response in both the presence and absence of amoxicillin or clavulanic acid. Basal tone, frequency, and amplitude of contractions were digitized and recorded.Results:The amplitude of the spontaneous contractions increased with amoxicillin. Inhibition of neuronal activity prevented this effect. Clavulanic acid did not affect the spontaneous contractions. Basal tone and the rate of contractions did not differ with either drug. Stimulation with carbachol in the presence of amoxicillin caused a statistically significant increase in the contractility compared with carbachol alone.Conclusions:Amoxicillin alters the spontaneous longitudinal mechanical activity of juvenile rat duodenum. Our results suggest that amoxicillin modulates the spontaneous pattern of cyclic mechanical activity of duodenal smooth muscle through noncholinergic, neurally mediated mechanisms. Our work provides an initial physiologic basis for the therapeutic use of amoxicillin in patients with gastrointestinal dysmotility.
Teaching Splinting Techniques Using a Just-in-Time Training Instructional Video
Authors: Cheng Yu-Tsun , Liu Deborah R. , Wang Vincent J. 
Published: April 2015

Objective
Splinting is a multistep procedure that is seldom performed by primary care physicians. Just-in-time training (JITT) is an emerging teaching modality and can be an invaluable asset for infrequently performed procedures or in locations where teaching resources and trained professionals are limited. Our objective was to determine the utility of JITT for teaching medical students the short-arm (SA) volar splinting technique.

Methods
This was a prospective randomized controlled pilot study. An instructional video on SA volar splinting was produced. Students viewed the video or had access to standard medical textbooks (control group) immediately before applying an SA volar splint. The students were assessed for the quality of the splint via a standard 6-point skills checklist. The times required for presplinting preparation and for completion of the splint were also measured.

Results
Just-in-time training group students scored higher on the splint checklist (mean [SD], 5.45 [1.06]; 95% confidence interval [CI], 4.99–5.92 vs mean [SD], 1.58 [1.12]; 95% CI, 1.04–2.12; P < 0.0001), had higher pass rates (73%; 95% CI, 53%–93% vs 0%; P < 0.0001), and required less time (minutes) for presplinting preparation (mean [SD], 7.86 [2.45]; 95% CI, 6.78–8.94 vs mean [SD], 9.89 [0.46]; 95% CI, 9.67–10.12; P < 0.0001) compared with the control group. No difference was seen in the time required to complete a splint, successful or not.

Conclusions
In comparison with reading standard textbooks, watching a brief JITT instructional video before splinting yielded faster learning times combined with more successful procedural skills. The use of a JITT instructional video may have potential applications, including globally, as an alternative resource for teaching and disseminating procedural skills, such as SA volar splinting.
Cultural Impact on Medication Instructions: The Case of the Turkish Teaspoon
Authors: Kannan Lakshmi , Blocher Nissa 
Published: April 2015

Abstract
Medication errors are preventable events related to inappropriate medication use that could potentially result in patient harm. Here we present a patient encounter that has exemplified the importance of appropriate communication and the inevitable role of every individual in ensuring appropriate prescription medication use. Multidisciplinary efforts are required to ensure patient safety in today’s systems based practice. This case highlights cultural barriers to the practice of medicine and the growing need to explore and address them appropriately.
The Cardioprotective Effect of Icariin on Ischemia–Reperfusion Injury in Isolated Rat Heart: Potential Involvement of the PI3K‐Akt Signaling Pathway
Authors: Ke Zunping , Liu Jingjing , Xu Peng , Gao Aimei , Wang Lei , Ji Lijuan 
Published: April 2015

SummaryAimsIcariin (ICA), a flavonoid isolated from epimedii, has been reported to have potential protective effects on the cardiovascular system. This study is to investigate the effect and the underlying mechanisms of ICA on ischemia/reperfusion (I/R) injury.MethodsWister rat hearts were subjected to I/R using Langendorff perfusion system. Cardiac function, myocardial infarct size, lactate dehydrogenase (LDH), and creatine kinase‐MB (CK‐MB) activities in coronary effluent, and superoxide dismutase (SOD) and malondialdehyde (MDA) content in heart tissue and cardiomyocyte apoptosis were assayed.ResultsCompared with the I/R group, ICA treatment significantly improved cardiac function, decreased myocardial infarct size, enzyme activity, oxidative stress, and apoptosis. In addition, ICA treatment lead to an increased p‐Akt level, which was partially reversed by LY294002, a PI3K pathway inhibitor.ConclusionOur study suggests that ICA has a cardioprotective effect against I/R injury, which is associated with its antioxidative and anti‐apoptotic effect, at least partially, through the activation of PI3K‐Akt signaling pathway.
Sociodemographic characteristics and attitudes towards motherhood among single women compared with cohabiting women treated with donor semen – a Danish multicenter study
Authors: Salomon Maria , Sylvest Randi , Hansson Helena , Nyboe Andersen Anders , Schmidt Lone 
Published: April 2015

AbstractObjectiveTo examine sociodemographic characteristics, family backgrounds, reproductive histories, and attitudes towards motherhood in single vs. cohabiting women seeking treatment with donor semen.DesignBaseline data collection in a multicenter cohort study.SettingAll nine public fertility clinics in Denmark.SampleIn total n = 311 childless women initiating assisted reproduction using donor semen.MethodsSelf‐reported questionnaire responses from n = 184 single women seeking treatment by using donor semen were compared with responses from n = 127 cohabiting women.Main outcome measuresSociodemographic characteristics, family backgrounds, reproductive histories, attitudes towards motherhood.ResultsSingle women were 3.5 years older on average when initiating treatment compared with cohabiting women. No significant differences were found regarding sociodemographic characteristics, previous long‐term relationships, previous pregnancies, or attitudes towards motherhood between single women and cohabiting women. The vast majority of single women wanted to achieve parenthood with a partner, 85.8% wished to have a partner in the future, and approximately half of them preferred for a partner to take parental responsibilities.ConclusionsIn this study single women seeking treatment with donor semen in the public health system did not differ from cohabiting women, except that they were older. To be a single mother by choice is not their preferred way of parenthood, but a solution they needed to accept.
Risk stratification with cervical length and fetal fibronectin in women with threatened preterm labor before 34 weeks and not delivering within 7 days
Authors: Hermans Frederik J.R. , Bruijn Merel M.C. , Vis Jolande Y. , Wilms Femke F. , Oudijk Martijn A. , Porath Martina M. , Scheepers Hubertina C.J. , Bloemenkamp Kitty W.M. , Bax Caroline J. , Cornette Jérôme M.J. , Nij Bijvanck Bas W.A. , Franssen Maureen T.M. , Vandenbussche Frank P.H.A. , Kok Marjolein , Grobman William A. , Van Der Post Joris A.M. , Bossuyt Patrick M.M. , Opmeer Brent C. , Mol Ben Willem J. , Schuit Ewoud , Van Baaren Gert‐Jan 
Published: April 2015

AbstractObjectiveTo stratify the risk of spontaneous preterm delivery using cervical length (CL) and fetal fibronectin (fFN) in women with threatened preterm labor who remained pregnant after 7 days.DesignProspective observational study.SettingNationwide cohort of women with threatened preterm labor from the Netherlands.PopulationWomen with threatened preterm labor between 24 and 34 weeks with a valid CL and fFN measurement and remaining pregnant 7 days after admission.MethodsKaplan–Meier and Cox proportional hazards models were used to estimate cumulative percentages and hazard ratios (HR) for spontaneous delivery.Main outcome measuresSpontaneous delivery between 7 and 14 days after initial presentation and spontaneous preterm delivery before 34 weeks.ResultsThe risk of delivery between 7 and 14 days was significantly increased for women with a CL < 15 mm or a CL ≥15 to <30 mm and a positive fFN, compared with women with a CL ≥30 mm: HR 22.3 [95% confidence interval (CI) 2.6–191] and 14 (95% CI 1.8–118), respectively. For spontaneous preterm delivery before 34 weeks the risk was increased for women with a CL < 15 mm [HR 6.3 (95% CI 2.6–15)] or with a CL ≥15 to <30 mm with either positive fFN [HR 3.6 (95% CI 1.5–8.7)] or negative fFN [HR 3.0 (95% CI 1.2–7.1)] compared with women with a CL ≥ 30 mm.ConclusionsIn women remaining pregnant 7 days after threatened preterm labor, CL and fFN results can be used in risk stratification for spontaneous delivery.
Support for down‐staging of pregnancy‐associated cervical cancer
Authors: Kärrberg Cecilia , Rådberg Thomas , Holmberg Erik , Norström Anders 
Published: April 2015

AbstractObjectiveTo evaluate all cases of cervical cancer associated with pregnancy during 16 years in the Western Region of Sweden.DesignRetrospective, descriptive cohort study.Setting and populationAll women with cervical cancer, diagnosed during pregnancy or within 6 months after parturition, between 1993 and 2008.MethodsThe study was based on data from different registers and medical records.Main outcome measuresIncidence, diagnostic measures, treatment and outcome of disease.ResultsCervical cancer was diagnosed in 47 women (15.6/100 000 deliveries). Sixteen women had abnormal vaginal bleeding and/or discharge. The other women were asymptomatic and diagnosed by abnormal cervical smear or clinical signs at vaginal examination. Nine women had atypical squamous cells of uncertain significance as presenting by cervical atypia. Twenty‐two women had stage IA, 17 stage IB1, six stage IB2 and two stage IIA cancer. Cancer was diagnosed in the first trimester in two, in the second trimester in 14, in the third trimester in five and postpartum in 26 women. Histology revealed squamous cell carcinoma in 36 women, adenocarcinoma in eight, and adenosquamous carcinoma in three. Twenty women underwent cesarean section due to diagnosed or clinically suspected cancer, combined with the Wertheim–Meigs radical hysterectomy in six women. Sixteen women with stage IA1 cancer without signs of vascular invasion underwent conization as definitive therapy. Six women died of the disease.ConclusionEarly detection of cervical cytological atypia and proper follow‐up during pregnancy led to detection of a high proportion of stage I cancer cases, which could be cured with fertility‐sparing therapy.
Presenting phenotype of paediatric inflammatory bowel disease in Wessex, Southern England 2010–2013
Authors: Ashton JJ , Coelho T , Ennis S , Batra A , Afzal NA , Beattie RM 
Published: April 2015

AbstractAimThere has been at least a twofold increase in the incidence of paediatric inflammatory bowel disease (PIBD) over the last 20 years; we report the presenting features from 2010 to 2013 and compare with previous data.MethodsAll patients diagnosed with PIBD at University Hospitals Southampton from 2010 to 2013 were identified from an in‐house database. Data were obtained from paper and electronic notes. Height, weight and BMI SDS are presented as median values (95% CI).ResultsOne hundred and seventy‐two patients were included (median age at diagnosis 13.5, 115 male); Crohn's disease (CD) – 107, UC – 50, inflammatory bowel disease unclassified (IBDU) – 15. The most common presenting features of CD were abdominal pain (86%), diarrhoea (78.5%) and weight loss (56.1%); 42.1% of patients had all three. In UC blood in stool (92%), diarrhoea (92%) and abdominal pain (88%) were the most common; all three in 76% of patients. CD presented with ileocolonic disease in 52.5%. UC presented with pancolitis in 64%. There was growth delay in CD: height −0.37 (−0.60 to −0.14); weight −1.09 (−1.35 to −0.83). Growth was maintained in UC: height 0.53 (0.19 to 0.87); weight 0.14 (−0.20 to 0.48).ConclusionPaediatric inflammatory bowel disease phenotype remains as extensive despite increasing incidence. Although the classical phenotype is common, a reasonable proportion present with atypical features, normal growth and normal blood markers.