bluuebunny/crossref_metadata_2025 huggingface dataset:
Maternal body composition in seedstock herds. 3. Multivariate analysis using factor analytic models and cluster analysis
Authors: De Faveri J. , Verbyla A. P. , Lee S. J. , Pitchford W. S.
Published: September 2017

Considerable information exists on genetic relationships of body composition and carcass quality of young and finished beef cattle. However, there is a dearth of information on genetic relationships of cow body composition over time and, also, relationships with young-animal body-composition measures. The aim of the present study is to understand genetic relationships among various cow body-composition traits of Angus cows over time, from yearling to weaning of a second calf at ~3.5 years. To determine genetic correlations among various composition traits over time, a multi-trait–multi-time analysis is required. For the Maternal Productivity Project, this necessitates modelling of five traits (namely weight and ultrasound measure for loin eye muscle area (EMA), rib fat, P8 rump fat and intramuscular fat) by five time combinations (recordings at yearling then pre-calving and weaning in first and second parity). The approach was based on including all 25 trait-by-time combinations in an analysis using factor analytic models to approximate the genetic covariance matrix. Various models for the residual covariance structure were investigated. The analyses yielded correlations that could be compared with those of past studies reported in the literature and, also, to a set of bivariate analyses. Clustering of the genetic multi-trait–multi-time correlation structure resulted in a separation of traits (weight and EMA, and the fat traits) and also of time effects into early (heifer = before first lactation) and late (cow = post-first lactation) measurements.
Effects of forage type and age at which forage provision is started on growth performance, rumen fermentation, blood metabolites and intestinal enzymes in Holstein calves
Authors: Wu Z. H. , Azarfar A. , Simayi A. , Li S. L. , Jonker A. , Cao Z. J.
Published: September 2017

The aim of this study was to determine the effects of two forage sources supplemented either from Day 3 or Day 15 of age on growth performance, rumen fermentation, blood metabolites, intestinal enzymes and incidence of diarrhoea in Holstein bull calves. Forty neonatal male Holstein calves (40.6 ± 5.8 kg BW) were randomly assigned to five treatments, with eight replicates each, including calves fed starter feed without any forage provision (Control; CON), and the same starter plus either chopped alfalfa hay started fed from Day 3 (AE) or Day 15 of age (AL) or chopped oat hay fed from Day 3 (OE) or Day 15 of age (OL). The study finished when all calves were weaned at 56 days of age. During the experimental period average daily gain, starter intake and total dry matter intake were similar among calves fed either of five dietary treatments (P > 0.05). Empty rumen weight (proportional to bodyweight) was greater in CON calves than in OL calves (P < 0.05). The AL calves had a lighter small intestine compared with CON, OL and AE calves, but similar to OE. Frequency of diarrhoea was not affected by dietary treatment (P > 0.05). Rumen concentration of total volatile fatty acids and pH were similar among dietary treatments (P > 0.05). Control calves had a lower molar proportion of acetate compared with OL calves, but similar to the other calves (P < 0.05). Forage-fed calves had similar molar proportion of butyrate to CON calves. Acetate to propionate ratio was higher in OL-fed calves than in those fed CON and AE diets (P < 0.05). Rumen concentration of NH3-N tended to be higher (P = 0.059) in CON calves than in forage-fed calves. During experimental period, serum concentrations of globulin, total protein, glucose and total cholesterol were similar among dietary treatments. Calves fed OE had lower serum concentration of albumin than those fed other diets (P < 0.01). Serum concentration of triglycerides (P < 0.05) was greater in calves fed AE followed by those fed AL and then those fed CON, OL and OE. The AL-fed calves had a higher serum lactate dehydrogenase compared with AE and OE fed calves, but similar to calves fed OL and CON. Duodenum amylase concentration was greater (P < 0.05) in AE-fed calves compared with CON-fed calves, but similar to calves fed AL, OL and OE. Calves fed OL had greater (P < 0.05) ileum lipase concentration than those fed OE, but similar to calves fed AL, AE and CON. In conclusion, provision of chopped alfalfa or oat hay to calves either from Day 3 or Day 15 of age resulted in similar starter intake and total dry matter intake and feed efficiency and physical development of the reticulorumen compared with calves fed the CON diet, which justifies the supply of forage to young calves, even at an early age, as forages are generally cheaper than starter concentrates.
Thinking hypothetically
Authors: Evans Jonathan St B. T.
Published: September 2017

A remarkable feature of human intelligence is our ability to think hypothetically. We can imagine how things might be in the future and how they might have turned out differently in the past. Imagination plays an important role in science, arts, and engineering, and is fundamental to rational decision making. A hypothesis is a supposition concerning some aspect of the world about us. Developing and testing hypotheses in an informal way is part of our everyday thinking. ‘Thinking hypothetically’ discusses hypothesis testing and scientific reasoning, introducing the concept of the mental model. It also discusses the Wason selection task—probably the most famous problem in the psychology of reasoning—as well as causal and counterfactual reasoning.
Decision making
Authors: Evans Jonathan St B. T.
Published: September 2017

We make a decision every time that we do something when we could have done something else, but most of these decisions are habitual and require little thought. ‘Decision making’ explains that hypothetical thinking is essential to deliberative decision making. The psychology of decision making has been much influenced by the study of economics, which provides a theory of rational decision making. This theory requires that people project future consequences of their choices, estimating probabilities and values and generally choosing the options with the best (mathematically) expected value. Against this we have a wealth of psychological evidence that both decision making and probability judgement are subject to a whole host of cognitive biases.
A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs
Authors: Kim Sun Ah , Cho Chang-Sung , Kim Suh-Ryung , Bull Shelley B , Yoo Yun Joo
Published: September 2017

Motivation

Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation.

Results

We present Big-LD, a block partition method based on interval graph modeling of LD bins which are clusters of strong pairwise LD SNPs, not necessarily physically consecutive. Big-LD uses an agglomerative approach that starts by identifying small communities of SNPs, i.e. the SNPs in each LD bin region, and proceeds by merging these communities. We determine the number of blocks using a method to find maximum-weight independent set. Big-LD produces larger LD blocks compared to existing methods such as MATILDE, Haploview, MIG ++, or S-MIG ++ and the LD blocks better agree with recombination hotspot locations determined by sperm-typing experiments. The observed average runtime of Big-LD for 13 288 240 non-monomorphic SNPs from 1000 Genomes Project autosome data (286 East Asians) is about 5.83 h, which is a significant improvement over the existing methods.

Availability and implementation

Source code and documentation are available for download at http://github.com/sunnyeesl/BigLD.

Supplementary information

Supplementary data are available at Bioinformatics online.
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
Authors: Lareau Caleb A , Aryee Martin J
Published: September 2017

The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state.

Availability and implementation

Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html

Supplementary information

Supplementary data are available at Bioinformatics online.
Expression of KIR2DS1 does not significantly contribute to NK cell cytotoxicity in HLA-C1/C2 heterozygous haplotype B donors
Authors: Baltner Karla , Kübler Ayline , Pal Marina , Balvočiūte Monika , Mezger Markus , Handgretinger Rupert , André Maya C
Published: September 2017

NK cells are functionally controlled by the killer immunoglobulin-like receptor (KIR) family that comprises inhibitory (iKIR) and activating (aKIR) members. Genetic association studies suggest that donors expressing aKIRs next to iKIRs will be superior donors in the setting of hematopoietic stem cell transplantation of patients with leukemia. However, contrary evidence states that aKIR expression may be irrelevant or even detrimental. Using a complex methodology incorporating KIR-Q-PCR, double fluorescence and viSNE analysis, we characterized subset distribution patterns and functionality in haplotype A donors which lack aKIRs and haplotype B donors that express a variety of B-specific genes. Here, we show that the alloreactive KIR2DS1+ NK cell subset in HLA-C1/C2 donors is highly responsive towards C2-expressing targets but quantitatively small and as such does not significantly contribute to cytotoxicity. Thus, we fail to find a direct link between haplotype allocation status and NK cell cytotoxicity at least in HLA-C1/C2 heterozygous donors.
DataMed – an open source discovery index for finding biomedical datasets
Authors: Chen Xiaoling , Gururaj Anupama E , Ozyurt Burak , Liu Ruiling , Soysal Ergin , Cohen Trevor , Tiryaki Firat , Li Yueling , Zong Nansu , Jiang Min , Rogith Deevakar , Salimi Mandana , Kim Hyeon-eui , Rocca-Serra Philippe , Gonzalez-Beltran Alejandra , Farcas Claudiu , Johnson Todd , Margolis Ron , Alter George , Sansone Susanna-Assunta , Fore Ian M , Ohno-Machado Lucila , Grethe Jeffrey S , Xu Hua
Published: September 2017

Objective

Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain.

Materials and Methods

DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health–funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium. It consists of 2 main components: (1) a data ingestion pipeline that collects and transforms original metadata information to a unified metadata model, called DatA Tag Suite (DATS), and (2) a search engine that finds relevant datasets based on user-entered queries. In addition to describing its architecture and techniques, we evaluated individual components within DataMed, including the accuracy of the ingestion pipeline, the prevalence of the DATS model across repositories, and the overall performance of the dataset retrieval engine.

Results and Conclusion

Our manual review shows that the ingestion pipeline could achieve an accuracy of 90% and core elements of DATS had varied frequency across repositories. On a manually curated benchmark dataset, the DataMed search engine achieved an inferred average precision of 0.2033 and a precision at 10 (P@10, the number of relevant results in the top 10 search results) of 0.6022, by implementing advanced natural language processing and terminology services. Currently, we have made the DataMed system publically available as an open source package for the biomedical community.
Antineutrophil cytoplasmic antibody-associated vasculitis and malignancy
Authors: Wester Trejo Maria A.C. , Bajema Ingeborg M. , van Daalen Emma E.
Published: September 2017

Purpose of review

Patients with antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) have an increased malignancy risk compared with the general population. This review aims to evaluate recent evidence for changes in the incidence of malignancy in patients with AAV and to examine explanations for the association between AAV and malignancy.

Recent findings

The overall malignancy risk in patients with AAV has decreased, most likely as a result of recent changes in therapeutic regimen, that is, a decrease in the exposure to cyclophosphamide. The risk of nonmelanoma skin cancer (NMSC), however, remains increased, which is probably attributable to treatment with azathioprine. Malignancy risk in patients with AAV treated with rituximab was found to be lower than in cyclophosphamide-treated patients. The incidence of malignancy prior to AAV is not increased compared with the general population.

Continuing efforts to reduce the exposure to cyclophosphamide have led to a decrease in malignancy risk in patients with AAV, except for NMSC. Rituximab could be a well tolerated alternative for cyclophosphamide regarding the development of malignancies.
Management of Preinvasive Lesions
Authors: PATRONO MARIA G. , CORZO CAMILA , INIESTA MARIA , RAMIREZ PEDRO T.
Published: September 2017

Serous tubal intraepithelial carcinoma is considered the precursor lesion of high-grade serous carcinoma, and found in both low-risk and high-risk populations. Isolated serous tubal intraepithelial carcinomas in patients with BRCA1/2 mutations are detected in ∼2% of patients undergoing risk-reducing bilateral salpingo-oophorectomy and even with removal of the tubes and ovaries the rate of developing primary peritoneal carcinoma following remains up to 7.5%. Postoperative recommendations after finding incidental STICs remain unclear and surgical staging, adjuvant chemotherapy, or observation have been proposed. Discovery of STIC should prompt consideration of hereditary cancer program referral for BRCA1/2 mutation screening.
OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY FEATURES OF ANGIOID STREAKS
Authors: Corbelli Eleonora , Carnevali Adriano , Marchese Alessandro , Cicinelli Maria Vittoria , Querques Lea , Sacconi Riccardo , Bandello Francesco , Querques Giuseppe
Published: September 2017

Purpose:

To analyze the optical coherence tomography angiography features of eyes affected with angioid streaks (AS) and to evaluate their ability to predict choroidal neovascularization (CNV) activity.

Methods:

Angioid streaks were individuated from a pool of consecutive patients. Eyes with and without CNV were evaluated by multimodal imaging.

Results:

Thirty-eight eyes of 19 consecutive patients diagnosed with AS were included. Thirty of 38 eyes with CNV and 8 of 38 eyes without CNV were included. In the majority of cases, CNV showed on optical coherence tomography angiography tangled appearance always associated with signs of neovascular inactivity on multimodal imaging (100%–0%, inactive-active, respectively). Choroidal neovascularization cases showing interlacing appearance were often associated with signs of neovascular activity on multimodal imaging (71.4%–28.6%, active-inactive, respectively). Optical coherence tomography angiography revealed a total of 27 AS, of which 20 appeared as a choriocapillary rarefaction, and in 7 AS, optical coherence tomography angiography choriocapillary segmentation revealed an irregular vascular network, possibly representing fibrovascular tissue over the crack-like breaks in Bruch membrane.

Conclusion:

Optical coherence tomography angiography is a noninvasive tool to detect the presence of CNV secondary to AS and to evaluate CNV activity. Optical coherence tomography angiography is able to add a novel element to the multimodal imaging characterization of AS.
Functional Morphology of the Lipid Layer of the Tear Film
Authors: Arita Reiko , Fukuoka Shima , Morishige Naoyuki
Published: September 2017

Meibomian glands secrete the oily layer of the tear film, which prevents excessive evaporation of tear fluid. Dysfunction of meibomian glands is not only one of the causes of evaporative dry eye but also one of the main causes of entire dry eye. To understand the pathophysiology of meibomian gland dysfunction, it is important to evaluate both the morphology and function of the meibomian gland. We previously reported that meibography enabled visualization of the morphology of the meibomian gland. Meanwhile, tear interferometry was introduced as an evaluation method for the function of the meibomian gland. We combined observations of the oily layer and the aqueous layer of the tear film and found that a tear film compensatory system may work toward maintenance of tear film homeostasis. In this review, we describe both morphological evaluation systems for the meibomian gland, including noninvasive meibography, and functional evaluation systems, including tear interferometry. We further describe the morphological changes of the meibomian glands in various ocular surface diseases. Finally, we demonstrate the concept of a tear film compensatory system and propose a method for tear film component-oriented diagnosis.
Single-Pass 4-Throw Pupilloplasty for Pre-Descemet Endothelial Keratoplasty
Authors: Narang Priya , Agarwal Amar , Kumar Dhivya A.
Published: September 2017

Purpose:

To describe the feasibility and applicability of the single-pass 4-throw pupilloplasty (SFT) technique in the Pre-Descemet endothelial keratoplasty (PDEK) procedure.

Methods:

In cases with endothelial decompensation and pupil deformity, SFT was performed to prevent the escape of air into the posterior segment. Fourier domain anterior segment optical coherence tomography was performed to analyze elevation of the iris and the suture tail end from the iris plane. In cases with aphakic bullous keratopathy, glued intrascleral (glued IOL) fixation was performed followed by SFT and PDEK, whereas in cases with pseudophakic bullous keratopathy due to malpositioned IOLs, the IOL was explanted followed by the glued IOL technique that was then followed by SFT with PDEK.

Results:

The procedure was performed in 9 eyes of 9 patients. The Fourier domain anterior segment optical coherence tomography image taken at the level of the iris demonstrated an elevation of the iris about 145 μm (longitudinal meridian, range 136–160 μm) and 165 μm (cross-section meridian, range 160–175 μm) from the adjoining iris plane. The end on view of the suture end was observed above the iris plane for about 47 μm (range 40–65 μm). Partial graft detachment was observed in 1 case. No incidence of primary graft failure or graft rejection during the entire follow-up period was reported in any of the eyes.

Conclusions:

SFT serves an effective technique for performing pupilloplasty in PDEK cases without the presence of a knot in the anterior chamber that poses a risk of mechanical damage to the donor graft.
The Glaucoma Italian Pediatric Study (GIPSy): 1-Year Results
Authors: Quaranta Luciano , Biagioli Elena , Riva Ivano , Galli Francesca , Poli Davide , Rulli Eliana , Katsanos Andreas , Longo Antonio , Uva Maurizio G. , Torri Valter , Weinreb Robert N.
Published: September 2017

Purpose:

To investigate the efficacy and safety of a treatment strategy with latanoprost and dorzolamide in primary pediatric glaucoma patients partially responsive to surgery.

Patients and Methods:

Children with primary pediatric glaucoma having postsurgical untreated intraocular pressure (IOP) between 22 and 26 mm Hg were eligible. At baseline, patients were administered latanoprost once daily. Depending on IOP reduction, patients were allocated to continuation of latanoprost monotherapy or addition of dorzolamide twice daily, or switch to dorzolamide monotherapy 3 times daily. Patients in the dorzolamide monotherapy group with IOP reduction <20% from baseline were considered nonresponders. The primary endpoint was the percentage of responders. Study treatment continued for 3 years or until treatment failure. The present article reports the 1-year analysis results.

Results:

A total of 35 patients (57 eyes) were analyzed. The mean age was 4.0 years (SD, 3.8). In total, 51 eyes were included in the efficacy analysis. In total, 43 eyes (84.3%; 95% confidence interval, 74.3-94.3) were considered responders: 29 on latanoprost monotherapy, 11 on the latanoprost/dorzolamide combination, and only 3 on the dorzolamide monotherapy. The efficacy of pharmacological treatment was inversely related to the age at the time of surgery. IOP reduction was 8.7 mm Hg (SD, 2.2) for latanoprost, 7.5 mm Hg (SD, 1.4) for the latanoprost/dorzolamide combination, and 8.7 mm Hg (SD, 2.1) for the dorzolamide monotherapy. Only mild or moderate local adverse events were noted. None of the patients was withdrawn due to adverse events.

Conclusion:

Latanoprost alone or in combination with dorzolamide is safe and highly effective in lowering IOP in children postsurgery. Nonresponders were mainly patients with early presentation of the disease.
Thinking About One's Feelings
Authors: Rinaldi Romina , Radian Viorica , Rossignol Mandy , Kandana Arachchige Kendra G. , Lefebvre Laurent
Published: September 2017

Alexithymia is described as a disturbance in the cognitive and affective processing of emotions. Little is known about the cognitive styles associated with this personality trait. In this article, we examine to what extent alexithymia is linked with poorer rational cognitive style. A total of 685 participants from a nonclinical sample completed the Toronto Alexithymia Scale–20 along with self-reported and behavioral measures of cognitive styles. Results suggest that people with a high level of self-reported alexithymia show lower rational abilities. The findings of this study extend previous work on cognitive processes underlying emotional self-regulation impairments in alexithymia, suggesting that these difficulties may be linked to a poorer use of rational process.
Radial Extracorporeal Shock Wave Therapy in an Individual With Primary Trigeminal Neuralgia
Authors: Zhang Dai , Meng Ying , Hai Hong , Yu Xiao Tong , Ma Yue Wen
Published: September 2017

A patient with primary trigeminal neuralgia exhibited pain relief without medication after radial extracorporeal shock wave therapy. The 52-yr-old woman had a 3-yr history of primary trigeminal neuralgia, involving the right maxillary division (V2) and the mandibular division (V3). She became refractory to carbamazepine and exhibited hepatic dysfunction. She hence received 3000 to 6000 impulses of craniofacial radial extracorporeal shock wave therapy to the region centered on the surface projection of the trigeminal ganglion and pain areas at 10 Hz; the intensity ranged from 1.4 to 4.5 bars twice per week for 8 wks. At baseline, and 1, 2, and 5 mos after treatment, the Barrow Neurological Institute scores were IV, IIIa, II, and II, and the visual analog scale scores were 8, 3, 1, and 1, respectively. No complications or adverse effects were observed. The hepatic function returned to normal after the discontinuation of carbamazepine. This case report demonstrates the feasibility of radial extracorporeal shock wave therapy for primary trigeminal neuralgia without complications or adverse effects with careful regulation of the therapy intensity.
Major Depressive Disorder in Patients With Doctoral Degrees: Patient-reported Depressive Symptom Severity, Functioning, and Quality of Life Before and After Initial Treatment in the STAR*D Study
Authors: STEINER ALEXANDER J. , BOULOS NATHALIE , WRIGHT STEPHANIE M. , MIROCHA JAMES , SMITH KIMBERLY , LÓPEZ ENRIQUE , GOHAR SHERIF H. , ISHAK WAGUIH W.
Published: September 2017

Objective:

This study examined patients with medical or doctoral degrees diagnosed with major depressive disorder (MDD) by analyzing patient-reported depressive symptom severity, functioning, and quality of life (QOL) before and after treatment of MDD.

Methods:

Analyses were conducted in a sample of 2280 adult outpatient participants with MDD from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study with complete entry and exit scores for the level 1 (citalopram monotherapy) trial. The sample contained 62 participants who had completed medical or doctoral degrees (DOCS) and 2218 participants without medical or doctoral degrees (non-DOCS). QOL was assessed with the Quality of Life Enjoyment and Satisfaction Questionnaire, functioning was assessed with the Work and Social Adjustment Scale, and depressive symptom severity was assessed with the Quick Inventory of Depressive Symptomatology-Self Report.

Results:

Both groups (DOCS and non-DOCS) had significant improvement in depressive symptom severity, functioning, and QOL following treatment (with equivalent improvements in mean change values). However, the DOCS group demonstrated larger effect sizes in symptom reduction for depression, increase in functioning, and improvement in QOL compared with the non-DOCS group. Participants who achieved remission from MDD at exit showed significantly greater improvement than nonremitters on functioning and QOL.

Conclusions:

Findings from this study indicated that, following citalopram monotherapy, the participants in the DOCS group achieved greater reductions in depressive symptom severity (based on effect sizes) than the participants in the non-DOCS group. For both treatment groups, the findings also showed the positive effect that remission status from MDD can have on QOL and functioning.
Blister Packaging Medication Increases Treatment Adherence in Psychiatric Patients
Authors: GUTIERREZ PETER M. , WORTZEL HAL S. , FORSTER JERI E. , LEITNER REBECCA A. , HOSTETTER TRISHA A. , BRENNER LISA A.
Published: September 2017

Objective:

To evaluate whether blister packing medications would improve prescription medication adherence in psychiatric patients. It was hypothesized that patients in the blister pack (BP) condition would be more adherent to their daily medications than those in the dispense as usual condition.

Methods:

This was a randomized trial involving up to 1 year of monthly follow-up assessments. Participants were recruited from an urban Veterans Affairs (VA) Medical Center in the Western United States. Inclusion criteria for participants included being diagnosed with a major affective disorder, posttraumatic stress disorder, schizophrenia, or a combination of these disorders; being 18 to 89 years of age; receiving prescription medications from the VA pharmacy; and being considered competent to manage their own medications. Of the 303 patients who consented to participate, 277 were randomized to 1 of the 2 study conditions, and 243 were retained in the study. The sample was 87% male, 47% white, with a mean age of 54.4 years. All medications prescribed and dispensed by the VA were either repackaged in monthly BPs or dispensed in standard pill vials.

Results:

The primary hypothesis was supported. Patients in the BPs condition showed evidence of better adherence at 12-month follow-up, as well as larger increases in adherence from 1 month to 12 months.

Conclusions:

Psychiatric patients adhere better to prescription medication regimens when receiving their medications in BP.
Predictors of Length of Stay in a Psychiatric Adolescent Treatment Program
Authors: REDDY RADHIKA , HA CAROLYN , NEWLIN ELIZABETH , SHARP CARLA
Published: September 2017

Understanding predictors of adolescent inpatient length of stay (LOS) is important in informing treatment outcomes for this age group. The current literature on adolescent LOS remains limited and has been characterized by methodological limitations. In the study described here, we examined a wide range of predictors for LOS in a psychiatric unit for adolescents (N=285), including severity of disorder (previous hospitalizations, self-harm, cognitive impairment and thought disorder, severe depression, history of trauma), types of psychotropic medication, and diagnoses. Our results indicated that LOS is associated with predictors that reflect psychiatric severity—most notably prescription of mood stabilizers and youth-reported internalizing symptoms.
High Prevalence of HIV Drug Resistance Among Newly Diagnosed Infants Aged <18 Months: Results From a Nationwide Surveillance in Nigeria
Authors: Inzaule Seth C. , Osi Samuels J. , Akinbiyi Gbenga , Emeka Asadu , Khamofu Hadiza , Mpazanje Rex , Ilesanmi Oluwafunke , Ndembi Nicaise , Odafe Solomon , Sigaloff Kim C. E. , Rinke de Wit Tobias F. , Akanmu Sulaimon
Published: September 2017

Background:

WHO recommends protease-inhibitor-based first-line regimen in infants because of risk of drug resistance from failed prophylaxis used in prevention of mother-to-child transmission (PMTCT). However, cost and logistics impede implementation in sub-Saharan Africa, and >75% of children still receive nonnucleoside reverse transcriptase inhibitor-based regimen (NNRTI) used in PMTCT.

Methods:

We assessed the national pretreatment drug resistance prevalence of HIV-infected children aged <18 months in Nigeria, using WHO-recommended HIV drug resistance surveillance protocol. We used remnant dried blood spots collected between June 2014 and July 2015 from 15 early infant diagnosis facilities spread across all the 6 geopolitical regions of Nigeria. Sampling was through a probability proportional-to-size approach. HIV drug resistance was determined by population-based sequencing.

Results:

Overall, in 48% of infants (205 of 430) drug resistance mutations (DRM) were detected, conferring resistance to predominantly NNRTIs (45%). NRTI and multiclass NRTI/NNRTI resistance were present at 22% and 20%, respectively, while resistance to protease inhibitors was at 2%. Among 204 infants with exposure to drugs for PMTCT, 57% had DRMs, conferring NNRTI resistance in 54% and multiclass NRTI/NNRTI resistance in 29%. DRMs were also detected in 34% of 132 PMTCT unexposed infants.

Conclusion:

A high frequency of PDR, mainly NNRTI-associated, was observed in a nationwide surveillance among newly diagnosed HIV-infected children in Nigeria. PDR prevalence was equally high in PMTCT-unexposed infants. Our results support the use of protease inhibitor-based first-line regimens in HIV-infected young children regardless of PMTCT history and underscore the need to accelerate implementation of the newly disseminated guideline in Nigeria.
An Unusual Location of Osteochondroma: Temporal Bone
Authors: Atalay Erdogan Banu , Cakan Dogan , Sanli Arif , Erdogan Ozgur , Safak Ayse Sezim , Elibol Vildan
Published: September 2017

Osteochondromas are the most common benign tumor of the bones which are cartilage-capped exophytic lesions that arises from the bone cortex. They usually seen in the axial skeleton, especially around the metaphysis of long bone but seldom in the head and neck region. The majority of patients in the head and neck region affect the mandibular area. To our knowledge, this is the first reported patient with an osteochondroma of the temporal bone in the English literature. A patient with temporal bone osteochondroma and its surgical treatment are here described.
Process and Outcome of Fecal Microbiota Transplants in Patients With Recurrent Clostridium difficile Infection
Authors: Walton Janice , Burns Denise , Gaehle Kay E.
Published: September 2017

The incidence of Clostridium difficile infection is on the rise worldwide, causing high mortality rates and costing patients, hospitals, and insurance companies millions of dollars annually. Fecal microbiota transplants successfully treat recurrent C. difficile infections unresponsive to standard pharmacologic treatment such as flagyl, vancomycin, or rifaximin. Evidence in the literature provided the foundation for the development and refinement of this fecal microbiota transplant protocol. During the initial phase of the project, the protocol included patient selection criteria, donor screening/selection, infection control, fecal processing and delivery, and patient pre and postprocedure education. This article highlights the second phase of prospective testing of a nurse-driven protocol to implement fecal microbiota transplantation in patients with recurrent C. difficile infection. All stages of the protocol are explained as well as rationale for component parts to achieve successful patient outcomes when the protocol is carefully followed.
Palliative and end-of-life care for adults with advanced chronic obstructive pulmonary disease: a rapid review focusing on patient and family caregiver perspectives
Authors: Mathews Gillian , Johnston Bridget
Published: September 2017

Purpose of review

The aim of the review was to explore patient and family caregiver perspectives on key issues for ensuring quality of end-of-life care for people with chronic obstructive pulmonary disease (COPD). The growing evidence on the value of specialist palliative care services demonstrates significant improvements in treatments and provisions; however, much of the literature is generic in nature or centred on people with a cancer diagnosis. In this review, we examine the literature to ascertain the views and needs of patients and carers affected by advanced COPD, a highly debilitating condition that can have a profoundly negative impact on the quality of end-of-life experience.

Recent findings

A total of 19 papers were included in the review. The main themes in the literature were Holistic Care, Illness Trajectory and Technology.

Areas of unmet need emphasized across physical, psychosocial and spiritual domains were identified, particularly in relation to appropriate and timely conversations. Positive developments in the care and treatment of advanced COPD include the use of the STIOLTO Respimat inhaler, a brief educative and psychosocial intervention based on cognitive-behavioural therapy, and high-intensity exercise training. There is some evidence regarding the use of technology in end-stage COPD.
Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for animal gut microbiomes
Authors: Videvall Elin , Strandh Maria , Engelbrecht Anel , Cloete Schalk , Cornwallis Charlie K.
Published: September 2017

The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of the direct PCR method for measuring host microbiomes has not yet been investigated other than in humans with 454-sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used MoBio PowerSoil DNA extraction kit in five distinct gut sample types (ileum – caecum – colon – faeces – cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in caecal, colon, and faecal samples. However, the two methods recovered significantly different microbiomes in cloacal, and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages, and found that both methods were highly consistent for caecal, colon, and faecal samples (rs> 0.7), but had low repeatability for cloacal (rs= 0.39) and ileal (rs= −0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S data, which will aid future gut microbiome studies of animals.
Evaluating Internal Model Strength and Performance of Myoelectric Prosthesis Control Strategies
Authors: Shehata Ahmed W. , Scheme Erik J. , Sensinger Jonathon W.
Published: September 2017

Ongoing developments in myoelectric prosthesis control have provided prosthesis users with an assortment of control strategies that vary in reliability and performance. Many studies have focused on improving performance by providing feedback to the user, but have overlooked the effect of this feedback on internal model development, which is key to improving long-term performance. In this work, the strength of internal models developed for two commonly used myoelectric control strategies: raw control with raw feedback (using a regression-based approach), and filtered control with filtered feedback (using a classifier-based approach), were evaluated using two psychometric measures: trial-by-trial adaptation and just-noticeable-difference. The performance of both strategies was also evaluated using a Schmidt’s style target acquisition task. Results obtained from 24 able-bodied subjects showed that although filtered control with filtered feedback had better short-term performance in path efficiency (p< 0.05), raw control with raw feedback resulted in stronger internal model development (p< 0.05), which may lead to better long-term performance. Despite inherent noise in the control signals of the regression controller, these findings suggest that rich feedback associated with regression control may be used to improve human understanding of the myoelectric control system.
A synthetic stroma-free germinal center niche using material-surface driven polyvalent signaling efficiently induces antigen-specific humoral immunityex vivo
Authors: Roh Kyung-Ho , Wilson Hannah K. , Pradhan Pallab , Bai Kevin , Bohannon Caitlin D. , Dale Gordon , Leleux Jardin , Jacob Joshy , Roy Krishnendu
Published: September 2017

B cells play a major role in the adaptive immune response by producing antigen-specific antibodies against pathogens and imparting immunological memory. Following infection or vaccination, antibody-secreting B cells and memory B cells are generated in specialized regions of lymph nodes and spleens, called germinal centers. Here, we report a fully syntheticex-vivosystem that recapitulates the generation of antigen-specific germinal-center (GC) like B cells using material-surface driven polyvalent signaling. This synthetic germinal center (sGC) reaction was effectively induced using biomaterial-based artificial “follicular T helper cells (TFH)” that provided both natural CD40-CD40L ligation as well as crosslinking of CD40; and by mimicking artificial “follicular dendritic cells (FDC)” to provide efficient, polyvalent antigen presentation. The artificial sGC reaction resulted in efficient B cell expansion, immunoglobulin (Ig) class switching, and expression of germinal center phenotypes. Antigen presentation during sGC reaction selectively enhanced the antigen-specific B cell population and induced somatic hyper-mutations for potential affinity maturation. The resulting B cell population consisted primarily of GC-like B cells (centrocytes) as well as some plasma-like B cells expressing CD138. With concurrent cell sorting, we successfully created highly enriched populations of antigen-specific B cells. Adoptive transfer of these GC-like B cells into non-irradiated isogeneic or non-lethally irradiated congenic recipient mice showed successful engraftment and survival of the donor cells for the 4 week test period. We show that this material-surface driven sGC reaction can be successfully applied to not only splenic B cells but also B cells isolated from more therapeutically relevant sources such as peripheral blood mononuclear cells (PBMCs), thus making our current work an exciting prospect in the new era of personalized medicine and custom-immunotherapy.
Stress granule-inducing eukaryotic translation initiation factor 4A inhibitors block influenza A virus replication
Authors: Slaine Patrick D. , Kleer Mariel , Smith Nathan , Khaperskyy Denys A. , McCormick Craig
Published: September 2017

Eukaryotic translation initiation factor 4A (eIF4A) is a helicase that facilitates assembly of the translation preinitiation complex by unwinding structured mRNA 5’ untranslated regions. Pateamine A (PatA) and silvestrol are natural products that disrupt eIF4A function and arrest translation, thereby triggering the formation of cytoplasmic aggregates of stalled preinitiation complexes known as stress granules (SGs). Here we examined the effects of eIF4A inhibition by PatA and silvestrol on influenza A virus (IAV) protein synthesis and replication in cell culture. Treatment of infected cells with either PatA or silvestrol at early times post-infection results in SG formation, arrest of viral protein synthesis and failure to replicate the viral genome. PatA, which irreversibly binds to eIF4A, sustained long-term blockade of IAV replication following drug withdrawal, and inhibited IAV replication at concentrations that had minimal cytotoxicity. By contrast, the antiviral effects of silvestrol were fully reversible; drug withdrawal caused rapid SG dissolution and resumption of viral protein synthesis. IAV inhibition by silvestrol was invariably associated with cytotoxicity. PatA blocked replication of genetically divergent IAV strains, suggesting common dependence on host eIF4A activity. This study demonstrates the feasibility of targeting core host protein synthesis machinery to prevent viral replication.

IMPORTANCE

Influenza A virus (IAV) relies on cellular protein synthesis to decode viral messenger RNAs. Pateamine A and silvestrol are natural products that inactivate an essential protein synthesis protein known as eIF4A. Here we show that IAV is sensitive to these eIF4A inhibitor drugs. Treatment of infected cells with pateamine A or silvestrol prevented synthesis of viral proteins, viral genome replication and release of infectious virions. The irreversible eIF4A inhibitor pateamine A sustained long-term blockade of viral replication, whereas viral protein synthesis quickly resumed after silvestrol was removed from infected cells. Prolonged incubation of either infected or uninfected cells with these drugs induced the programmed cell death cascade called apoptosis. Our findings suggest that core components of the host protein synthesis machinery are viable targets for antiviral drug discovery. The most promising drug candidates should selectively block protein synthesis in infected cells without perturbing bystander uninfected cells.
Bdellovibrioand like organisms bacterial predators are not equally distributed in peri-alpine lakes
Authors: Paix Benoit , Jacquet Stéphan
Published: September 2017

Microbes drive a variety of ecosystem processes and services but still many of them remain largely unexplored because of our lack of knowledge on both diversity and functionality of some potentially key microbiological compartments. This is typically the case with and within the group of bacterial predators collectively known asBdellovibrioand like organisms (BALOs). Here we report for the first time the abundance, distribution and diversity of the three main families of these natural and obligatory predators of gram negative bacteria in three peri-alpine lakes (e.g. lakes Annecy, Bourget and Geneva) at different depths (surfacevs. 45 or 50 m) and along a few months (from August 2015 to January 2016). We show that, using PCR-DGGE and cloning-sequencing approaches, the diversity appeared relatively low and very specific to fresh waters or even of the lakes themselves. While thePeredibacteraceaefamily was represented mainly by a single species (i.e.Peredibacter starii), it could constitute up to 7% of the total bacterial cell abundances. Comparati vel y, the abundances of the two other families (referred to asBdellovibrionaceaeandBacteriovaracaceae) were significantly lower. More interestingly, the distribution in the water column was very different between the three groups suggesting various life strategies/niches for each of them:Peredibactereaceadominated near surface while theBdellovibrionaceaeand theBacteriovaracaceaewere more abundant at depth. All in all, our results suggest that these bacterial predators are likely to play a significant role in mortality, carbon fluxes and prokaryotic community structure in lakes.
A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel’s second law
Authors: Veller Carl , Kleckner Nancy , Nowak Martin A.
Published: September 2017

Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. However, such studies have been ham-pered by the fact that there has been no direct measure of this quantity. Existing measures consider crossing over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate because the positions of crossovers along a chromosome are also critical: a crossover towards the middle of a chromosome causes more shuffling than a crossover towards the tip. More-over, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel’s second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameterr̅as the probability that the alleles at two randomly chosen loci will be shuffled in the production of a gamete. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact thatr̅is larger when crossovers are more evenly spaced, which suggests a novel selective advantage of crossover interference. Utilization ofr̅is enabled by powerful emergent methods for determining crossover positions, either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that: (i)r̅in humans is close to its maximum possible value of 1/2, (ii) this high level of shuffling is due almost entirely to independent assortment, whose contribution is ~30 times greater than that of crossovers.