bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple Screening Tool to Help Identify High-Risk Children for Targeted HIV Testing in Malawian Inpatient Wards
Authors: Moucheraud Corrina , Chasweka Dennis , Nyirenda Mike , Schooley Alan , Dovel Kathryn , Hoffman Risa M. ,   on behalf of the EQUIP Innovations Team
Published: July 2018

Background:
To meet global AIDS goals, pediatric HIV diagnosis must be strengthened. Provider-initiated testing and counseling, which is recommended by the WHO, faces persistent implementation challenges in low-resource settings. Alternative approaches are needed.

Setting:
Malawi has achieved high coverage of HIV diagnosis and treatment, but there are gaps among pediatric populations. This study assessed the sensitivity and specificity of a brief screening tool to identify at-risk pediatric patients for targeted HIV testing in Malawi.

Methods:
A tool containing 6 yes/no items was used for children (aged 1–15 years) in the inpatient pediatric wards at 12 hospitals in Malawi (July 2016–July 2017). Questions were based on an established tool, translated to Chichewa, and implemented by HIV diagnostic assistants. All participating children were provided HIV testing and counseling per Ministry of Health guidelines. Analysis estimated the tool's characteristics including sensitivity, specificity, negative, and positive predictive values.

Results:
HIV prevalence among the 8602 participants was 1.1% (n = 90). Children with a screening tool score of 1 had double the odds of being HIV positive than those with a score of 0. Frequent sickness was the most sensitive predictor of HIV status (55.1%), and having a deceased parent was the most specific (96.7%). False classification of HIV-negative status was rare (n = 14) but occurred more often among boys and younger children.

Conclusions:
A brief screening tool for pediatric inpatients helped target HIV testing in those most at risk in a low-pediatric-prevalence, resource-constrained setting. Future research should include a direct, rigorous comparison with PITC including comparative effectiveness, efficiency, and cost effectiveness.
Associating Liver Partition and Portal Vein Ligation for Staged Hepatectomy for Unresectable Hepatitis B Virus-related Hepatocellular Carcinoma
Authors: Wang Zheng , Peng Yuanfei , Hu Jingwu , Wang Xiaoying , Sun Huichuan , Sun Jian , Shi Yinghong , Xiao Yongsheng , Ding Zhenbing , Yang Xinrong , Tang Min , Tang Zhaoyou , Wang Jiping , Lau Wan Y. , Fan Jia , Zhou Jian 
Published: July 2018

Objective:
The aim of the study is to assess the efficacy and safety of associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) in patients with hepatitis B virus-related hepatocellular carcinoma (HCC).

Background:
ALPSS allows curative resection of conventionally-unresectable liver tumors. However, its role in HCC is largely unknown.

Methods:
Consecutive HCC patients who underwent ALPPS at our center between April 2013 and September 2017 were retrospectively studied. The oncological results were compared with patients receiving transcatheter arterial chemoembolization (TACE), and patients undergoing one-stage resection by using propensity score matching (PSM) analysis.

Results:
The median tumor diameter was 13 cm (range: 6–22 cm) in patients with a single tumor (n = 28), whereas the median total tumor diameter was 12 cm (range: 9–31 cm) in patients with multiple tumors (n = 17). After stage-1 ALPPS, the median future liver remnant (FLR) increased by 56.8%. The stage-2 ALPPS was completed in 41 patients (91.1%) after a median of 12 days. The 90-day mortality rate was 11.1% (5/45). The overall survival (OS) rates at 1- and 3-year were 64.2% and 60.2%, whereas the disease-free survival (DFS) rates at 1 and 3 years were 47.6% and 43.9%, respectively. On PSM analysis, the long-term survival of patients undergoing ALPPS was significantly better than those receiving TACE (OS, P = 0.004; DFS, P < 0.0001) and similar to those subjected to one-stage liver resection (OS, P = 0.514; DFS, P = 0.849).

Conclusions:
The long-term survival after ALPPS was significantly better than TACE, and similar to those after one-stage liver resection. ALPPS is a viable treatment option for patients with unresectable HCC in selected patients.
Clinical Importance of Mean Corpuscular Volume as a Prognostic Marker After Esophagectomy for Esophageal Cancer
Authors: Yoshida Naoya , Kosumi Keisuke , Tokunaga Ryuma , Baba Yoshifumi , Nagai Yohei , Miyamoto Yuji , Iwagami Shiro , Iwatsuki Masaaki , Hiyoshi Yukiharu , Ishimoto Takatsugu , Eto Kojiro , Imamura Yu , Watanabe Masayuki , Baba Hideo 
Published: July 2018

Objective:
To elucidate the clinical value of mean corpuscular volume (MCV) for prognostic prediction in patients with esophageal cancer who underwent radical esophagectomy.

Background:
High MCV is suggested to be relevant to the incidence and prognosis of several malignancies. However, few studies investigating the correlation between MCV and survival outcome of esophageal cancer have been conducted.

Methods:
This study included 570 patients with esophageal cancer who underwent radical esophagectomy between April, 2005 and December, 2017. Patients were divided into 2 groups according to the standard value of pretreatment MCV: normal (83–99 fL) and high (>99 fL) groups. Clinical backgrounds, short-term outcomes, and prognostic outcomes postesophagectomy were retrospectively compared between the groups.

Results:
Of all patients, 410 (71.9%) had normal MCV, and 160 (28.1%) had high MCV. High MCV was significantly associated with lower body mass index, higher frequency of habitual alcohol and tobacco use, and higher incidence of multiple primary malignancies other than esophageal cancer. High MCV also correlated with higher incidence of postoperative morbidity of the Clavien–Dindo classification ≥II and pulmonary morbidity. Overall survival was significantly worse in patients with high MCV. Multivariate analysis suggested that high MCV was an independent risk factor for worse survival outcome (hazard ratio 1.54, 95% confidence interval 1.098–2.151, P = 0.012).

Conclusions:
Patients with high MCV have various disadvantages in clinical background that can adversely affect both short-term and long-term outcomes after esophagectomy. MCV can become a predictive marker to estimate survival outcome after esophagectomy for esophageal cancer.
Short-term aerobic training does not improve memory functioning in relapsing remitting multiple sclerosis – a randomized controlled trial
Authors: Baquet L , Hasselmann H , Patra S , Stellmann JP , Vettorazzi E , Engel AK , Rosenkranz S , Poettgen J , Gold SM , Schulz KH , Heesen C 
Published: July 2018

AbstractBackgroundOnly few aerobic exercise intervention trials specifically targeting cognitive functioning have been performed in MS.Objective and methodsThis randomized controlled trial aimed to determine the effects of aerobic exercise on cognition in relapsing-remitting MS. The primary outcome was verbal memory (Verbal learning and memory test, VLMT). Patients were randomized to an intervention group (IG) program or a waitlist control group (CG). Patients in the IG exercised according to an individually tailored training schedule (with 2-3 sessions per week for 12 weeks). The primary analysis was carried out using the intention-to-treat (ITT) sample with ANCOVA adjusting for baseline scores.Results77 RRMS patients were screened and 68 participants randomized (CG n=34; IG n=34). The sample comprised 68% females, had a mean age of 39 years, a mean disease duration of 6.3 years, and a mean EDSS of 1.8. No significant effects were detected in the ITT analysis for the primary endpoint VLMT or any other cognitive measures. Moreover, no significant treatment effects were observed for quality of life, fatigue, or depressive symptoms.ConclusionThis study failed to demonstrate beneficial effects of aerobic exercise on cognition in RRMS.The trial was prospectively registered at clinicaltrials.gov (NCT02005237).
Closed-Loop Control of Active Sensing Movements Regulates Sensory Slip
Authors: Biswas Debojyoti , Arend Luke A. , Stamper Sarah A. , Vágvölgyi Balázs P. , Fortune Eric S. , Cowan Noah J. 
Published: July 2018

SummaryActive sensing involves the production of motor signals for the purpose of acquiring sensory information [1–3]. The most common form of active sensing, found across animal taxa and behaviors, involves the generation of movements—e.g. whisking [4–6], touching [7,8], sniffing [9,10], and eye movements [11]. Active-sensing movements profoundly affect the information carried by sensory feedback pathways [12–15] and are modulated by both top-down goals (e.g. measuring weight vs. texture [1,16]) and bottom-up stimuli (e.g. lights on/off [12]) but it remains unclear if and how these movements are controlled in relation to the ongoing feedback they generate. To investigate the control of movements for active sensing, we created an experimental apparatus for freely swimming weakly electric fish,Eigenmannia virescens, that modulates the gain of reafferent feedback by adjusting the position of a refuge based on real time videographic measurements of fish position. We discovered that fish robustly regulate sensory slip via closed-loop control of active-sensing movements. Specifically, as fish performed the task of maintaining position inside the refuge [17–22], they dramatically up- or down-regulated fore-aft active-sensing movements in relation to a 4-fold change of experimentally modulated reafferent gain. These changes in swimming movements served to maintain a constant magnitude of sensory slip. The magnitude of sensory slip depended on the presence or absence of visual cues. These results indicate that fish use two controllers: one that controls the acquisition of information by regulating feedback from active sensing movements, and another that maintains position in the refuge, a control structure that may be ubiquitous in animals [23,24].
Risk of bias in Cochrane systematic reviews: assessments of risk related to attrition bias are highly inconsistent
Authors: Babic Andrija , Tokalic Ruzica , Cunha João Amílcar Silva , Novak Ivana , Suto Jelena , Vidak Marin , Miosic Ivana , Vuka Ivana , Pericic Tina Poklepovic , Puljak Livia 
Published: July 2018

AbstractBackgroundAn important part of the systematic review methodology is appraisal of the risk of bias in included studies. Cochrane systematic reviews (CSRs) are considered golden standard regarding systematic review methodology, but Cochrane’s instructions for assessing risk of attrition bias are vague, which may lead to inconsistencies in authors’ assessments. The aim of this study was to analyze consistency of judgments and support for judgments of attrition bias in CSRs of interventions published in the Cochrane Database of Systematic Reviews (CDSR).MethodsWe analyzed CSRs published from July 2015 to June 2016 in the CDSR. We extracted data on number of included trials, judgment of attrition risk of bias for each included trial (low, unclear or high) and accompanying support for the judgment (supporting explanation). We also assessed how many CSRs had different judgments for the same supporting explanations.ResultsIn the main analysis we included 10292 judgments and supporting explanations for attrition bias from 729 CSRs. We categorized supporting explanations for those judgments into four categories and we found that most of the supporting explanations were unclear. Numerical indicators for percent of attrition, as well as statistics related to attrition were judged very differently. One third of CSR authors had more than one category of supporting explanation; some had up to four different categories. Inconsistencies were found even with the number of judgments, names of risk of bias domains and different judgments for the same supporting explanations in the same CSR.ConclusionWe found very high inconsistency in methods of appraising risk of attrition bias in recent Cochrane reviews. Systematic review authors need clear guidance about different categories they should assess and judgments for those explanations. Clear instructions about appraising risk of attrition bias will improve reliability of the Cochrane’s risk of bias tool, help authors in making decisions about risk of bias and help in making reliable decisions in healthcare.
Judgments of risk of bias associated with random sequence generation in trials included in Cochrane systematic reviews are frequently erroneous
Authors: Barcot Ognjen , Boric Matija , Pericic Tina Poklepovic , Cavar Marija , Dosenovic Svjetlana , Vuka Ivana , Puljak Livia 
Published: July 2018

AbstractBackgroundPurpose of this study was to analyze adequacy of judgments about risk of bias (RoB) for random sequence generation in Cochrane systematic reviews (CSRs) of randomized controlled trials (RCTs).MethodsInformation was extracted from RoB tables of CSRs using automated data scraping. We categorized all comments provided as supports for judgments for RoB related to randomization. We analyzed number and type of various supporting comments and assessed adequacy of RoB judgment for randomization in line with recommendations from the Cochrane Handbook.ResultsWe analyzed 10527 RCTs that were included in 729 CSRs. For 5682 RCTs randomization was not described; for the others it was indicated randomization was done using computer/software/internet (N=2886), random number table (N=888), mechanic method (N=366), or it was incomplete/inappropriate (N=303).Overall, 1194/10125 trials (12%) had erroneous RoB judgment about randomization. The highest proportion of errors was found for trials with high RoB (28%), followed by those with low (19%), or unclear (3%). Therefore, one in eight judgments for the analyzed domain in CSRs was erroneous, and one in three if the judgment was “high risk”.ConclusionCochrane systematic reviews cannot be necessarily trusted when it comes to judgments for risk of bias related to randomized sequence generation.
Cancer eQTLs can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity
Authors: Geeleher Paul , Nath Aritro , Wang Fan , Zhang Zhenyu , Barbeira Alvaro N. , Fessler Jessica , Grossman Robert L. , Seoighe Cathal , Huang R. Stephanie 
Published: July 2018

AbstractExpression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both. Here, we demonstrate a method to identify eQTLs affecting expression in cancer cells by modeling the statistical interaction between genotype and tumor purity. Only one-third of breast cancer risk variants, identified as eQTLs from a conventional analysis, could be confidently attributed to cancer cells. The remaining variants could affect cells of the tumor microenvironment, such as immune cells and fibroblasts. Deconvolution of tumor eQTLs will help determine how inherited polymorphisms influence cancer risk, development, and treatment response.
Single-cell and neuronal network alterations in an in vitro model of Fragile X syndrome
Authors: Moskalyuk Anastasiya , Kooy R. Frank , Giugliano Michele 
Published: July 2018

AbstractThe Fragile X mental retardation protein (FMRP) is involved in many cellular processes and it regulates synaptic and network development in neurons. Its absence is known to lead to intellectual disability, with a wide range of co-morbidities including autism. Over the past decades, FMRP research focused on abnormalities both in glutamatergic and GABAergic signalling, and an altered balance between excitation and inhibition has been hypothesised to underlie the clinical consequences of absence of the protein. Using FMRP knockout mice, we studied an in vitro model of cortical microcircuitry and observed that the loss of FMRP largely affected the electrophysiological correlates of network development and maturation but caused less alterations in single-cell phenotypes. Using a mathematical model, we demonstrated that the combination of an increased excitation and reduced inhibition describes best predicts our experimental observations during the ex vivo formation of the network connections.
Stable memory and computation in randomly rewiring neural networks
Authors: Acker Daniel , Paradis Suzanne , Miller Paul 
Published: July 2018

AbstractOur brains must maintain a representation of the world over a period of time much longer than the typical lifetime of the biological components producing that representation. For example, recent research suggests that dendritic spines in the adult mouse hippocampus are transient with an average lifetime of approximately 10 days. If this is true, and if turnover is equally likely for all spines, approximately 95-percent of excitatory synapses onto a particular neuron will turn over within 30 days; however, a neuron’s receptive field can be relatively stable over this period. Here, we use computational modeling to ask how memories can persist in neural circuits such as the hippocampus and visual cortex in the face of synapse turnover. We demonstrate that Hebbian learning during replay of pre-synaptic activity patterns can integrate newly formed synapses into pre-existing memories. Further, we find that Hebbian learning during replay is sufficient to stabilize the receptive fields of hippocampal place cells in a model of the grid-cell-to-place-cell transformation in CA1 and of orientation-selective cells in a model of the center-surround-to-simple-cell transformation in V1. We also ask how synapse turnover affects memory in Hopfield networks with CA3-like, auto-associative properties. We find that attractors of Hopfield networks are remarkably stable if learning occurs during network reactivations. Together, these data suggest that a simple learning rule, correlative Hebbian plasticity of synaptic strengths, is sufficient to preserve neural representations in the face of synapse turnover, even in the absence of Hebbian structural plasticity.
TnClone: high-throughput clonal analysis using Tn5-mediated library construction and de novo assembly
Authors: Hwang Byungjin , Heo Sunghoon , Cho Namjin , Bang Duhee 
Published: July 2018

ABSTRACTA typical molecular cloning procedure requires Sanger sequencing for validation, which becomes cost-prohibitive and labour-intensive for large-scale clonal analysis of genotype-phenotype studies. Here we present a Tn5-mediated clonal analysis platform TnClone, which uses next-generation sequencing (NGS) to rapidly and cost-effectively analyze a large number of clones. We also developed a user-friendly graphical user interface and have provided general guidelines for conducting validation experiments. Using TnClone, we achieved more than 20-fold cost reduction compared with the cost incurred using conventional Sanger sequencing and detected low-frequency mutant clones (~10%) in mixed samples. We tested our programme and achieved 99.4% sensitivity. Our platform provides rapid turnaround with minimal hands-on time for secondary evaluation as NGS technology continues to evolve.
Regeneration of dopaminergic neurons in adult zebrafish depends on immune system activation and differs for distinct populations
Authors: Caldwell Lindsey J. , Davies Nick O. , Cavone Leonardo , Mysiak Karolina S. , Semenova Svetlana A. , Panula Pertti , Armstrong J. Douglas , Becker Catherina G. , Becker Thomas 
Published: July 2018

ABSTRACTAdult zebrafish regenerate neurons in their brain, but the extent and variability of this capacity is unclear. Here we ask whether loss of various dopaminergic neuron populations is sufficient to trigger their functional regeneration. Genetic lineage tracing shows that specific diencephalic ependymo-radial glial progenitor cells (ERGs) give rise to new dopaminergic (Th+) neurons. Ablation elicits an immune response, increased proliferation of ERGs and increased addition of new Th+ neurons in populations that constitutively add new neurons, e.g. diencephalic population 5/6. Inhibiting the immune response attenuates neurogenesis to control levels. Boosting the immune response enhances ERG proliferation, but not addition of Th+ neurons. In contrast, in populations in which constitutive neurogenesis is undetectable, e.g. the posterior tuberculum and locus coeruleus, cell replacement and tissue integration are incomplete and transient. This is associated with loss of spinal Th+ axons, as well as permanent deficits in shoaling and reproductive behaviour. Hence, dopaminergic neuron populations in the adult zebrafish brain show vast differences in regenerative capacity that correlate with constitutive addition of neurons and depend on immune system activation.
Identifying Lineage-specific Targets of Darwinian Selection by a Bayesian Analysis of Genomic Polymorphisms and Divergence from Multiple Species
Authors: Zhao Shilei , Zhang Tao , Liu Qi , Liu Yongming , Wu Hao , Su Bing , Shi Peng , Chen Hua 
Published: July 2018

AbstractWe present a method that jointly analyzes the polymorphism and divergence sites in genomic sequences of multiple species to identify the genes under positive or negative selection and pinpoints the occurrence time of selection to a specific lineage of the species phylogeny. This method integrates population genetics models using the Bayesian Poisson random field framework and combines information over all gene loci to boost the power to detect selection. The method provides posterior distributions of the fitness effects of each gene along with parameters associated with the evolutionary history, including the species divergence times and effective population sizes of external species. A simulation is performed, and the results demonstrate that our method provides accurate estimates of these population genetic parameters.The proposed method is applied to genomic sequences of humans, chimpanzees, gorillas and orangutans, and a spatial and temporal map is constructed of the natural selection that occurred during the evolutionary history of the four Hominidae species. In addition to FOXP2 and other known genes, we identify a new list of lineage-specific targets of Darwinian selection. The positively selected genes in the human lineage are enriched in pathways of gene expression regulation, immune system, metabolism etc. Interestingly, some pathways, such as gene expression, are significantly enriched with positively selected genes, whereas other pathways, such as metabolism, are enriched with both positively and negatively selected genes. Our analysis provides insights into Darwinian evolution in the coding regions of humans and great apes and thus serves as a basis for further molecular and functional studies.