bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urinary Tract Infection in Children With Nephrotic Syndrome
Authors: Narain Upma , Gupta Arvind 
Published: August 2017

Background:
The occurrence of urinary tract infection (UTI) in nephrotic syndrome has been reported. However, the only causes for the infection reported to date are bacteria and prior reported series did not identify yeast or fungi as causative organisms.

Methods:
A retrospective study of 2880 children with nephrotic syndrome was made to determine the incidence of UTI, predisposing factor and bacterial and fungal etiologies.

Results:
Between January 2000 and November 2016, we identified that 15% of the children developed UTI. Within this group, bacterial UTI and fungal UTI were 84.0% and 16.0%, respectively. The genus Klebsiella (25.33%) predominates among bacteria, while Candida cruzi (26.08%) predominates among fungal etiologies. Statistical analysis was performed for biochemical indices and UTI and was found significant for low serum albumin and high serum cholesterol (P ≤ 0.05).

Conclusion:
This study emphasizes the importance of UTI in children and can be underdiagnosed in children with nephrotic syndrome because steroid therapy is anti-inflammatory and can mask the symptoms of UTI.
The Individual Experience of Aging Patients and the Current Service Provision in the Context of Italian Forensic Psychiatry: A Case Study
Authors: Di Lorito Claudio , Castelletti Luca , Tripi Giuseppa , Gandellini Maria Gloria , Dening Tom , Völlm Birgit 
Published: August 2017

ABSTRACT

Introduction
After the recent development of residential units for the execution of security measures managed by the National Health Service and the closing down of forensic psychiatric hospitals, no study has been conducted to investigate the individual experience of aging patients and to assess whether the new service is adequately meeting their needs. We aimed to explore the experience of the service of a sample of patients aged 50 years and above living in one of the Italian residential units for the execution of security measures.

Methods
We adopted a case study design and included a sample of five patients. We collected their basic demographic data, administered the Camberwell Assessment Needs Forensic Short Version and carried out in-depth qualitative semi-structured interviews.

Results
Results from the Camberwell Assessment Needs Forensic Short Version evidenced that met needs were more prevalent than unmet needs. The qualitative interviews demonstrated high levels of satisfaction around accommodation, healthcare provision, activities, availability of benefits and company, and lower levels of satisfaction around psychological and practical support.

Discussion
This study gave voice to aging forensic psychiatric patients and provided through personal accounts, based on their lived experience, preliminary evidence around the benefits and limitations of the Italian residential forensic psychiatric system for this age group. Implications for clinical nursing forensic practitioners operating within different service frameworks are discussed.
Rehabilitation of an Individual with Transfemoral Amputation Combining Aquatic Ambulation With Prosthetic Socket Incorporating High-Fidelity Skeletal Capture
Authors: Cutler Thomas J. 
Published: August 2017

ABSTRACT

Introduction
The High-Fidelity skeletal capture socket has shown promise in improving outcomes for persons with transfemoral amputation. This case report looks at a synergistic benefit when incorporating aquatic therapy with successful skeletal capture subischial transfemoral socket fitting. Although previous studies have shown some transfemoral prosthetic sockets to be ineffective as preserving femoral adduction angle, knee disarticulation level and high-fidelity transfemoral level sockets were not assessed, both of which use skeletal capture.

Case Presentation
A 64-year-old, 290-lb male individual with amputation had been unsuccessfully fit with six ischial containment suction sockets without skeletal capture over a 3-year period. Multiple complications, including a 45° hip flexion contracture and 100-ft maximum ambulation range, limited his rehabilitation.

Management and Outcome
Aquatic ambulation increased in-therapy walking time from 5 to 45 minutes. Thirty-day results included prosthetic side hip flexion contracture reduction from 45° to 20° ambulation range increased from 100 to 400 ft. The 120–day results showed contracture reduced to 12° and ambulation range to greater than 500 ft. Additional 120-day outcomes included disability rating reduction from 78% to 48% and Tinetti fall score increase from 10 of 28 to 17 of 28.

Discussion
Initial success with socket fit revealed limitations in certain approaches to rehabilitation of persons with amputation that were overcome in a reduced gravity environment. By combining both the additional reported stability benefit of the High-Fidelity Interface and the increased duration and confidence provided by the aquatic-based ambulation, the outcomes exceeded those anticipated with land-based ambulation alone.

Conclusion
By considering skeletal capture, the case report challenges the assumption that socket design cannot secure the femur and provide better outcomes. By having success in a reduced-gravity environment, one concludes that a scrutiny of the goals of transfemoral amputation is warranted.
Brief Report: Weight Gain in Persons With HIV Switched From Efavirenz-Based to Integrase Strand Transfer Inhibitor–Based Regimens
Authors: Norwood Jamison , Turner Megan , Bofill Carmen , Rebeiro Peter , Shepherd Bryan , Bebawy Sally , Hulgan Todd , Raffanti Stephen , Haas David W. , Sterling Timothy R. , Koethe John R. 
Published: August 2017

Background:
With the introduction of integrase strand transfer inhibitor (INSTI)-based antiretroviral therapy, persons living with HIV have a potent new treatment option. Recently, providers at our large treatment clinic noted weight gain in several patients who switched from efavirenz/tenofovir disoproxil fumarate/emtricitabine (EFV/TDF/FTC) to dolutegravir/abacavir/lamivudine (DTG/ABC/3TC). In this study, we evaluated weight change in patients with sustained virologic suppression who switched from EFV/TDF/FTC to an INSTI-containing regimen.

Methods:
We performed a retrospective observational cohort study among adults on EFV/TDF/FTC for at least 2 years who had virologic suppression. We assessed weight change over 18 months in patients who switched from EFV/TDF/FTC to an INSTI-containing regimen or a protease inhibitor (PI)-containing regimen versus those on EFV/TDF/FTC over the same period. In a subgroup analysis, we compared patients switched to DTG/ABC/3TC versus raltegravir- or elvitegravir-containing regimens.

Results:
A total of 495 patients were included: 136 who switched from EFV/TDF/FTC to an INSTI-containing regimen and 34 switched to a PI-containing regimen. Patients switched to an INSTI-containing regimen gained an average of 2.9 kg at 18 months compared with 0.9 kg among those continued on EFV/TDF/FTC (P = 0.003), whereas those switched to a PI regimen gained 0.7 kg (P = 0.81). Among INSTI regimens, those switched to DTG/ABC/3TC gained the most weight at 18 months (5.3 kg, P = 0.001 compared with EFV/TDF/FTC).

Conclusion:
Adults living with HIV with viral suppression gained significantly more weight after switching from daily, fixed-dose EFV/TDF/FTC to an INSTI-based regimen compared with those remaining on EFV/TDF/FTC. This weight gain was greatest among patients switching to DTG/ABC/3TC.
Brief Report: Lopinavir Hair Concentrations Are the Strongest Predictor of Viremia in HIV-Infected Asian Children and Adolescents on Second-Line Antiretroviral Therapy
Authors: Pintye Jillian , Bacchetti Peter , Teeraananchai Sirinya , Kerr Stephen , Prasitsuebsai Wasana , Singtoroj Thida , Kuncze Karen , Louie Alexander , Koss Catherine A. , Jin Chengshi , Phung Nhi , Horng Howard , Sohn Annette H. , Gandhi Monica 
Published: August 2017

Background:
Children/adolescents display suboptimal antiretroviral therapy (ART) adherence and outcomes versus adults. Hair ART concentrations are objective adherence measures that predict viremia in adults but longitudinal data on hair levels in pediatric populations is limited. We assessed the predictive utility of hair lopinavir (LPV) levels on viremia among youth on second-line ART.

Methods:
We examined predictors of viremia (HIV-1 RNA >400 and >1000 copies/mL) at least 24 weeks after switch to LPV-based second-line ART in a cohort of HIV-infected Asian children followed between 2011 and 2014. Small hair samples, HIV-1 RNA, and self-reported adherence were collected biannually. Hair concentrations of LPV were measured through liquid chromatography/tandem mass spectrometry using validated methods. Time-to-first viremia was examined using discrete-time Cox models.

Results:
Overall, 244 children met the inclusion criteria for the present analysis. Approximately half (55%) were boys and the median age 10 years [interquartile range (IQR) 7–13]; 40% were older than 11 years. At switch to second-line ART, median CD4 count was 300 (IQR 146–547) cells/mm3 and median HIV-RNA level was 5.0 (IQR 4.3–5.6) log10/mL. Median time of study follow-up was 48 weeks and a median of 3 (range 1–5) hair samples were collected from each participant. Adjusting for age, sex, country, self-reported adherence, CD4, and HIV-RNA, higher LPV hair concentrations were the strongest predictor of lower odds of viremia (HIV-RNA >400 copies/mL adjusted odds ratio = 0.41 per doubling in hair concentration, 95% confidence interval: 0.29 to 0.58, P < 0.001; HIV-RNA >1000 copies/mL, adjusted odds ratio = 0.54, 95% confidence interval: 0.45 to 0.65, P < 0.001).

Conclusions:
Hair concentrations predict viremia among children with HIV on second-line ART and could guide clinical decisions for this population.
Infiltrative Hepatocellular Carcinoma With Portal Vein Tumor Thrombosis Treated With a Single High-Dose Y90 Radioembolization and Subsequent Liver Transplantation Without a Recurrence
Authors: Dendy Meaghan S. , Camacho Juan C. , Ludwig Johannes M. , Krasinskas Alyssa M. , Knechtle Stuart J. , Kim Hyun S. 
Published: August 2017

Background
Infiltrative hepatocellular carcinoma with macrovascular invasion is a relatively rare presentation and usually fatal disease.

Methods
Both patients exceeded Milan and University of California-San Francisco (UCSF) criteria, and per Barcelona Clinic Liver Cancer group guidelines, they were enrolled in a prospective open-label radioembolization phase II trial that gave them optimized lobar doses of Yttrium-90 as solely the first-line therapy without concomitant or additional pharmacological or locoregional therapies.

Results
Three months after radioembolization, the patients demonstrated no residual viable disease on surveillance imaging. The patients were then followed up with serial imaging for 2 years in 3-month intervals, without documenting recurrence or extrahepatic disease. Finally, both patients underwent transplantation and after more than 20 months of imaging surveillance, no locoregional or systemic recurrence have been observed.

Conclusions
We present, to our knowledge, the first 2 reports of transplantation after successfully downstaging infiltrative disease with portal vein tumoral thrombosis, which traditionally poses as a relative contraindication for resection or transplantation.
Influence of HLA Matching on the Efficacy of Allogeneic Mesenchymal Stromal Cell Therapies for Osteoarthritis and Degenerative Disc Disease
Authors: García-Sancho Javier , Sánchez Ana , Vega Aurelio , Noriega David C. , Nocito Mercedes 
Published: August 2017

Background
The necessity for more effective therapies for chronic osteoarticular diseases has led to the development of treatments based on mesenchymal stem cells (MSCs), the natural precursors of musculoskeletal tissue. Treatments with autologous MSCs yielded excellent results, with nearly 70% improvement of pain and disability in osteoarthritis and degenerative disc disease. Using allogeneic MSCs is logistically more convenient and would widen the pool of eligible patients, but potential immune rejection should be considered. In this context, MSCs are purportedly immune evasive and better tolerated than other cell types.

Methods
We used samples collected during the performance of 2 randomized clinical trials using allogeneic bone marrow MSCs for treatment of osteoarthritis (NCT01586312) and degenerative disc disease (NCT01860417). Serum samples were used to determine anti-HLA antibodies, whereas either blood or MSC samples were used for HLA typing of recipients and donors, respectively. Algofunctional indexes were used as indicators of clinical evolution, and the correlation between the number of donor-host HLA mismatches and the efficacy of treatment was determined.

Results
Immune response was weak and transient, with reactivity decaying during the first year. Consistently, better donor-recipient HLA matching did not enhance efficacy.

Conclusions
This lack of reactivity is presumably due to the cooperation of 2 factors, (1) downregulation of the host immune responses by the transplanted MSCs and (2) effective insulation of these cells inside the articular cavity or the intervertebral disc, respectively. Interestingly, better HLA matching did not enhance efficacy. These observations have medical relevance as they support the clinical use of allogeneic cells, at least as a single-dose administration. Multiple-dose applications will require further research to exclude possible sensitization.
Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions
Authors: Silvas Tania V. , Hou Shurong , Myint Wazo , Somasundaran Mohan , Kelch Brian A. , Matsuo Hiroshi , Yilmaz Nese Kurt , Schiffer Celia A. 
Published: August 2017

ABSTRACTThe APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, substrate secondary structure, and pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), and found that A3A binds RNA in a sequence specific manner. Furthermore, A3A bound tighter to its substrate binding motif when in a loop compared to linear oligonucleotide. Our results suggest that the A3A affinity and preference for substrate is modulated by the structure of DNA, and not just its chemical identity. Analysis of previously published co-crystal structures of A3A bound to ssDNA in light of the above findings directed the proposal of a new model for the molecular mechanism underlying A3A sequence preference. On a broader scale, the results of this work not only provide key insights into the mechanism of A3’s beneficial roles in the cell, especially in viral restriction, but also into A3’s deleterious activity such as in the development of cancer.
A Method for Quantifying Molecular Interactions Using Stochastic Modelling and Super-Resolution Microscopy
Authors: Bermudez-Hernandez Keria , Keegan Sarah , Whelan Donna R. , Reid Dylan A. , Zagelbaum Jennifer , Yin Yandong , Ma Sisi , Rothenberg Eli , Fenyö David 
Published: August 2017

AbstractWe introduce the Interaction Factor (IF), a measure for quantifying the interaction of molecular clusters in super-resolution microscopy images. The IF is robust in the sense that it is independent of cluster density, and it only depends on the extent of the pair-wise interaction between different types of molecular clusters in the image. The IF for a single or a collection of images is estimated by first using stochastic modelling where the locations of clusters in the images are repeatedly randomized to estimate the distribution of the overlaps between the clusters in the absence of interaction (IF=0). Second, an analytical form of the relationship between IF and the overlap (which has the random overlap as its only parameter) is used to estimate the IF for the experimentally observed overlap. The advantage of IF compared to conventional methods to quantify interaction in microscopy images is that it is insensitive to changing cluster density and is an absolute measure of interaction, making the interpretation of experiments easier. We validate the IF method by using both simulated and experimental data and provide an ImageJ plugin for determining the IF of an image.
A High Performance, Inexpensive Setup for Simultaneous Multisite Recording of Electrophysiological Signals and Wide-Field Optical Imaging in the Mouse Cortex
Authors: Contreras Edgar Bermudez , Chekhov Sergey , Tarnowsky Jennifer , Sun Jianjun , McNaughton Bruce L. , Mohajerani Majid H. 
Published: August 2017

AbstractSimultaneous recording of optical and electrophysiological signals from multiple cortical areas may provide crucial information to expand our understanding of cortical function. However, the insertion of multiple electrodes into the brain may compromise optical imaging by both restricting the field of view, and interfering with the approaches used to stabilize the specimen. Existing methods that combine electrophysiological recording and optical imagingin vivoimplement either multiple surface electrodes or a single electrode for deeper recordings. To address such limitation, we built a microelectrode array (hyperdrive) compatible with wide-field imaging that allows insertion of up to 12 probes into a large brain area (8 mm diameter). The developed hyperdrive is comprised of a circle of individual microdrives where probes are positioned at an angle leaving a large brain area unobstructed for wide-field imaging. Multiple tetrodes and voltage-sensitive dye imaging (VSDI) were used for simultaneous registration of spontaneous and evoked cortical activity. The electrophysiological signals were used to extract local field potential (LFP) traces, multiunit and single-unit spiking activity. To demonstrate our approach, we compared LFP and VSD signals over multiple regions of the cortex and analyzed the relationship between single-unit and global cortical population activities. The study of the interactions between cortical activity at local and global scales, such as the one presented in this work, can help to expand our knowledge of brain function.
Deep Recurrent Neural Network Reveals a Hierarchy of Process Memory during Dynamic Natural Vision
Authors: Shi Junxing , Wen Haiguang , Zhang Yizhen , Han Kuan , Liu Zhongming 
Published: August 2017

ABSTRACTThe human visual cortex extracts both spatial and temporal visual features to support perception and guide behavior. Deep convolutional neural networks (CNNs) provide a computational framework to model cortical representation and organization for spatial visual processing, but unable to explain how the brain processes temporal information. To overcome this limitation, we extended a CNN by adding recurrent connections to different layers of the CNN to allow spatial representations to be remembered and accumulated over time. The extended model, or the recurrent neural network (RNN), embodied a hierarchical and distributed model of process memory as an integral part of visual processing. Unlike the CNN, the RNN learned spatiotemporal features from videos to enable action recognition. The RNN better predicted cortical responses to natural movie stimuli than the CNN, at all visual areas especially those along the dorsal stream. As a fully-observable model of visual processing, the RNN also revealed a cortical hierarchy of temporal receptive window, dynamics of process memory, and spatiotemporal representations. These results support the hypothesis of process memory, and demonstrate the potential of using the RNN for in-depth computational understanding of dynamic natural vision.
Weighted likelihood inference of genomic autozygosity patterns in dense genotype data
Authors: Blant Alexandra , Kwong Michelle , Szpiech Zachary A. , Pemberton Trevor J. 
Published: August 2017

AbstractBackgroundGenomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to detect ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns.ResultsWe report a weighted likelihood approach for identifying ROA in dense genotype data that accounts for autocorrelation among genotyped positions and the possibilities of unobserved mutation and recombination events, and variability in the confidence of individual genotype calls in whole genome sequence (WGS) data. Forward-time genetic simulations under two demographic scenarios that reflect situations where inbreeding and its effect on fitness are of interest suggest this approach is better powered than existing state-of-the-art methods to detect ROA at marker densities consistent with WGS and popular microarray genotyping platforms used in human and non-human studies. Moreover, we present evidence that suggests this approach is able to distinguish ROA arising via consanguinity from ROA arising via endogamy. Using subsets of The 1000 Genomes Project Phase 3 data we show that, relative to WGS, intermediate and long ROA are captured robustly with popular microarray platforms, while detection of short ROA is more variable and improves with marker density. Worldwide ROA patterns inferred from WGS data are found to accord well with those previously reported on the basis of microarray genotype data. Finally, we highlight the potential of this approach to detect genomic regions enriched for autozygosity signals in one group relative to another based upon comparisons of per-individual autozygosity likelihoods instead of inferred ROA frequencies.ConclusionsThis weighted likelihood ROA detection approach can assist population- and disease-geneticists working with a wide variety of data types and species to explore ROA patterns and to identify genomic regions with differential ROA signals among groups, thereby advancing our understanding of evolutionary history and the role of recessive variation in phenotypic variation and disease.
Structure and diversity of urinary cell-free DNA informative of host-pathogen interactions in human urinary tract infection
Authors: Burnham Philip , Dadhania Darshana , Heyang Michael , Chen Fanny , Westblade Lars F. , Suthanthiran Manikkam , Lee John Richard , De Vlaminck Iwijn 
Published: August 2017

AbstractInfections of the urinary tract are the most common form of infection in the human population. Here, we tested the utility of urinary cell-free DNA (cfDNA) to comprehensively monitor host and pathogen dynamics in the scope of bacterial and viral urinary tract infections. We assayed cfDNA isolated from 141 urine samples obtained from a cohort of 82 kidney transplant recipients by next-generation sequencing. We find that urinary cfDNA simultaneously informs about the composition of the bacterial and viral components of the microbiome, antimicrobial susceptibility, bacterial growth dynamics, kidney allograft injury, and the host response to infection. These different layers of information are accessible from a single assay and individually agree with corresponding clinical tests based on quantitative PCR, conventional bacterial culture, and urinalysis. In addition, cfDNA reveals the frequent occurrence of pathologies that remain undiagnosed in conventional diagnostic workups. Our work identifies urinary cfDNA as a highly versatile tool to monitor infections of the urinary tract.