bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attrition from HIV treatment after enrollment in a differentiated service delivery model: a cohort analysis of routine care in Zambia
Authors: Jo Youngji , Jamieson Lise , Phiri Bevis , Grimsrud Anna , Mwansa Muya , Shakwelele Hilda , Haimbe Prudence , Mukumbwa-Mwenechanya Mpande , Mulenga Priscilla Lumano , Nichols Brooke E , Rosen Sydney 
Published: June 2022

AbstractBackgroundMany sub-Saharan Africa countries are scaling up differentiated service delivery (DSD) models for HIV treatment to increase access and remove barriers to care. We assessed factors associated with attrition after DSD model enrollment in Zambia, focusing on patient-level characteristics.MethodsWe conducted a retrospective record review using electronic medical records (EMR) of adults (≥15 years) initiated on antiretroviral (ART) between 01 January 2018 and 30 November 2021. Attrition was defined as lost to follow-up (LTFU) or died by November 30, 2021. We categorized DSD models into eight groups: fast-track, adherence groups, community pick-up points, home ART delivery, extended facility hours, facility multi-month dispensing (MMD, 4–6-month ART dispensing), frequent refill care (facility 1-2 month dispensing), and conventional care (facility 3 month dispensing, reference group). We used Fine and Gray competing risk regression to assess patient-level factors associated with attrition, stratified by sex and rural/urban setting.ResultsOf 547,281 eligible patients, 68% (n=372,409) enrolled in DSD models, most commonly facility MMD (n=306,430, 82%), frequent refill care (n=47,142, 13%), and fast track (n=14,433, 4%), with <2% enrolled in the other DSD groups. Retention was higher in nearly all DSD models for all dispensing intervals, compared to the reference group, except fast track for the ≤2 month dispensing group. Retention benefits were greatest for patients in the extended clinic hours group and least for fast track dispensing.ConclusionAlthough retention in HIV treatment differed by DSD type, dispensing interval, and patient characteristics, nearly all DSD models out-performed conventional care. Understanding the factors that influence the retention of patients in DSD models could provide an important step towards improving DSD implementation.
Impact of Subthalamic Nucleus Stimulation on Urinary Dysfunction and Constipation in Parkinson’s Disease
Authors: Askari Asra , Zhu Brandon , Lam Jordan , Wyant Kara , Chou Kelvin , Patil Parag 
Published: June 2022

ABSTRACTIntroductionThe effect of subthalamic nucleus deep brain stimulation (STN DBS) on urinary dysfunction and constipation in Parkinson’s disease (PD) is variable. This study aims to identify potential surgical and non-surgical variables predicting their outcome.MethodsWe used the Movement Disorder Society-Unified PD Rating Scale (MDS-UPDRS) Part I to assess urinary dysfunction (item 10) and constipation (item 11) preoperatively and 6-12 months postoperatively. A multiple linear regression model was used to investigate the impact of Global Cerebral Atrophy (GCA) and active electrode contact location on the urinary dysfunction and constipation follow-up score, controlling for age, disease duration, baseline score, motor improvement, and levodopa-equivalent dose changes. An electric field model was applied to localize the maximal effect-site for constipation and urinary dysfunction compared to motor improvement.ResultAmong 74 patients, 23 improved, 28 deteriorated, and 23 remained unchanged for urinary dysfunction; 25 improved, 15 deteriorated, and 34 remained unchanged for constipation. GCA score and age significantly predicted urinary dysfunction follow-up score (R2 = 0.36, P<0.001). Increasing GCA and age independently were associated with worsening urinary symptoms. Disease duration, baseline constipation score, and anterior active electrode contacts in both hemispheres were significant predictors for constipation follow-up score (R2 =0.31, P<0.001). Higher baseline constipation score and disease duration were associated with worsening constipation; anterior active contact location was associated with improvement in constipation.ConclusionAnterior active contact locations are associated with improvement in constipation in PD patients after STN DBS. PD patients with greater GCA scores before surgery were more likely to experience urinary deterioration after DBS.
Dorsal Subthalamic Deep Brain Stimulation Improves Pain in Parkinson’s Disease
Authors: Askari Asra , Lam Jordan , Zhu Brandon J. , Lu Charles , Chou Kelvin L. , Wyant Kara J. , Patil Parag G. 
Published: June 2022

ABSTRACTIntroductionInconsistent effects of subthalamic deep brain stimulation (STN DBS) on pain, a common non-motor symptom of Parkinson’s disease (PD), may be due to variations in active contact location relative to a pain-reducing locus of stimulation.ObjectiveTo distinguish the loci of maximal effect for pain and motor improvement in the STN region.MethodsWe measured Movement Disorder Society Unified PD Rating Scale (MDS-UPDRS) Part I pain score (item-9), and MDS-UPDRS Part III motor score, preoperatively and 6-12 months after STN DBS. An ordinary least-squares regression model was used to examine active contact location as a predictor of follow-up pain score while controlling for baseline pain, age, dopaminergic medication, and motor improvement. An atlas-independent electric field model was applied to distinguish sites of maximally effective stimulation for pain and motor improvement.ResultsIn 74 PD patients, mean pain score significantly improved after STN DBS (p = 0.01). In a regression model, more dorsal active contact location was the only significant predictor of pain improvement (R2 = 0.17, p = 0.03). The stimulation locus for maximal pain improvement was lateral, anterior, and dorsal to that for maximal motor improvement.ConclusionsMore dorsal STN DBS improves pain. Stimulation of the zona incerta, a region known to modulate pain in humans, may explain this observation.
Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure
Authors: Vicente Anna Luiza Silva Almeida , Novoloaca Alexei , Cahais Vincent , Awada Zainab , Cuenin Cyrille , Spitz Natália , Carvalho André Lopes , Evangelista Adriane Feijó , Crovador Camila Souza , Reis Rui Manuel , Herceg Zdenko , de Lima Vazquez Vinicius , Ghantous Akram 
Published: June 2022

AbstractUltraviolet radiation (UV) is causally linked to cutaneous melanoma, yet the underlying epigenetic mechanisms, known as molecular sensors of exposure, have never been characterized in clinical biospecimen. Here, we integrate clinical and epigenome (DNA methylome), genome and transcriptome profiling of 112 cutaneous melanoma from two multi-ethnic cohorts. We identify UV-related alterations in regulatory regions and immunological pathways, with multi-OMICs cancer driver potential affecting patient survival.TAPBP, the top gene, is critically involved in immune function and encompasses several UV-altered methylation sites that were validated by targeted sequencing, providing cost-effective opportunities for clinical application. The DNA methylome also reveals non UV-related aberrations underlying pathological differences between the cutaneous and 17 acral melanomas. Unsupervised epigenomic mapping demonstrated that non UV-mutant cutaneous melanoma more closely resembles acral rather than UV-exposed cutaneous melanoma, with the latter showing better patient prognosis than the other two forms. These gene-environment interactions reveal translationally impactful mechanisms in melanomagenesis.
DRUG-RESISTANT TUBERCULOSIS CASE-FINDING STRATEGIES: A SCOPING REVIEW PROTOCOL
Authors: van Wyk Susanna S , Nliwasa Marriott , Seddon James A , Hoddinott Graeme , Viljoen Lario , Nepolo Emmanuel , Günther Gunar , Ruswa Nunurai , Lin Hsien-Ho , Niemann Stefan , Gandhi Neel , Shah Sarita , Claassens Mareli 
Published: June 2022

ABSTRACTBackgroundTransmission of drug-resistant tuberculosis (TB) is ongoing, and many households face catastrophic costs when a member is diagnosed and treated for drug-resistant TB. Finding individuals with drug-resistant TB and initiating treatment as early as possible is important to improve patient clinical outcomes and to break the chain of transmission to help control the pandemic.To our knowledge systematic reviews assessing effectiveness, cost-effectiveness, acceptability and feasibility of different drug-resistant TB case-finding strategies to inform research, policy and practice, have not been conducted and it is unknown whether enough research exists to conduct such reviews. It is also unknown whether case-finding strategies are similar for drug-resistant TB and drug-susceptible TB and whether we can draw on findings from drug-susceptible reviews to inform decisions on drug-resistant TB case-finding strategies.MethodsThe question for our review is: what literature is available on drug-resistant TB case finding and which case-finding strategies are described? We will look at studies that have sought to improve drug-resistant TB case detection. We will search the academic databases of CENTRAL, MEDLINE and EMBASE using no language or date restrictions. We will apply broad criteria for screening titles, abstracts and full text articles. A data extraction form will be developed in excel and applied to all primary research reports to collect standard information on each study. We will provide a narrative report with supporting figures and/or tables to summarize the data. A systems-based logic model, developed from a synthesis of drug-susceptible TB case-finding strategies, will be used as a framework to describe different strategies, resulting pathways and enhancements of pathways.DiscussionThis scoping review will chart existing literature on drug-resistant TB case finding and identify priority question(s) for a systematic review. It will also describe drug-resistant TB case-finding strategies and how they fit into a model of drug-susceptible TB case-finding pathways. The review will guide further research to inform decisions on drug-resistant TB case finding policy and practice.
SARS-COV-2 Delta and Omicron community transmission networks
Authors: Murray John M. , Murray Daniel D. , Schvoerer Evelyne , Akand Elma H. 
Published: June 2022

AbstractTo date, calculations of SARS-CoV-2 transmission networks at a population level have not been performed. Networks that estimate infections between individuals and whether this results in a mutation, can evaluate fitness of a mutational clone by how much it expands in number as well as determining the likelihood a transmission results in a new variant.Transmission networks of SARS-CoV-2 infection between individuals in Australia were estimated for Delta and Omicron variants using a novel method. Many of the sequences were identical, with clone sizes following power law distributions driven by negative binomial probability distributions for both the number of infections per individual and the number of mutations per transmission (mean 1.0 nucleotide change for Delta and 0.79 for Omicron). Using these distributions, an agent based model was able to replicate the observed clonal network structure, providing a basis for more detailed COVID-19 modelling. Recombination events, tracked by insertion/deletion (indel) patterns, occurred for each variant in these outbreaks. The residue at position 142 in the S open reading frame (ORF), frequently changed between G and D for Delta sequences, but this was independent of other mutations. On the other hand, several Omicron mutations were significantly connected across different ORF. This model reveals key transmission characteristics of SARS-CoV-2 and may complement traditional contact tracing and other public health strategies. This methodology can also be applied to other diseases as genetic sequencing of viruses becomes more commonplace.Author summaryAs SARS-COV-2 spreads through a community, it can mutate and generate new variants. How likely this is to occur and how much a particular viral clone expands, can indicate mutational probabilities and whether some mutations are fitter than others. By better understanding these aspects, future predictions can more accurately encapsulate possible changes in the epidemic within a community. We have developed a new method for piecing together the individual SARS-COV-2 cases that have been sequenced, to generate the structure of transmissions and mutational clones for an outbreak. While this method can be applied to other virus epidemics given sufficient sequenced data, we apply it to Delta and Omicron outbreaks in Australia. Interestingly, transmissions between individuals frequently do not result in mutations, with some clones growing very large. We characterise the probability that a mutation will occur, and track how these changes lead to sequential mutations in these outbreaks.
Auditory grouping ability predicts speech-in-noise performance in cochlear implants
Authors: Choi Inyong , Gander Phillip E. , Berger Joel I. , Hong Jean , Colby Sarah , McMurray Bob , Griffiths Timothy D. 
Published: June 2022

AbstractObjectivesCochlear implant (CI) users exhibit a large variance in understanding speech in noise (SiN). Past works in CI users found that spectral and temporal resolutions correlate with the SiN ability, but a large portion of variance has been remaining unexplained. Our group’s recent work on normal-hearing listeners showed that the ability of grouping temporally coherent tones in a complex auditory scene predicts SiN ability, highlighting a central mechanism of auditory scene analysis that contributes to SiN. The current study examined whether the auditory grouping ability contributes to SiN understanding in CI users as well.Design47 post-lingually deafened CI users performed multiple tasks including sentence-in-noise understanding, spectral ripple discrimination, temporal modulation detection, and stochastic figure-ground task in which listeners detect temporally coherent tone pips in the cloud of many tone pips that rise at random times at random frequencies. Accuracies from the latter three tasks were used as predictor variables while the sentence-in-noise performance was used as the dependent variable in a multiple linear regression analysis.ResultsNo co-linearity was found between any predictor variables. All the three predictors exhibited significant contribution in the multiple linear regression model, indicating that the ability to detect temporal coherence in a complex auditory scene explains a further amount of variance in CI users’ SiN performance that was not explained by spectral and temporal resolution.ConclusionsThis result indicates that the across-frequency comparison builds an important auditory cognitive mechanism in CI users’ SiN understanding. Clinically, this result proposes a novel paradigm to reveal a source of SiN difficulty in CI users and a potential rehabilitative strategy.
Retrospective behavioral sampling (RBS): a method to effectively track the cognitive fluctuations driven by naturalistic stimulation
Authors: Brandman Talia , Malach Rafael , Simony Erez 
Published: June 2022

AbstractEveryday experiences are dynamic, driving fluctuations across simultaneous cognitive processes. A key challenge in the study of naturalistic cognition is to disentangle the complexity of these dynamic processes, without altering the natural experience itself. Retrospective behavioral sampling (RBS) is a novel approach to track the cognitive fluctuations throughout the time-course of naturalistic stimulation, across a variety of cognitive dimensions. We tested the effectiveness and reliability of RBS in a web-based experiment, in which 53 participants viewed short movies and listened to a story, followed by retrospective reporting. Participants recalled their experience of 55 discrete events from the stimuli, rating their quality of memory, magnitude of surprise, intensity of negative and positive emotions, perceived importance, reflectivity state, and mental time travel. In addition, a subset of the original cohort re-rated their memory of events in a follow-up questionnaire. Results show highly replicable fluctuation patterns across distinct cognitive dimensions, thereby revealing a stimulus-driven experience that is substantially shared among individuals. Remarkably, memory ratings more than a week after stimulation resulted in an almost identical time-course of memorability as measured immediately following stimulation. In addition, idiosyncratic response patterns were preserved across different stimuli, indicating that RBS characterizes individual differences that are stimulus invariant. The current findings highlight the potential of RBS as a powerful tool for measuring dynamic processes of naturalistic cognition. We discuss the promising approach of matching RBS fluctuations with dynamic processes measured via other testing modalities, such as neuroimaging, to study the neural manifestations of naturalistic cognitive processing.
Assessing germline mutational profile and its clinicopathological associations in Triple Negative Breast Cancer
Authors: John Jisha , Bapat Ashwini , Gahlaut Siddharth , Luke Naveen , Kumar Rahul , Thakur Yashaswi , Konnur Aishwarya , Namewar Namrata , Reddy Ruhi , Shaikh Shaheen , Banale Rituja , Nagarkar Sanket , Nare Smeeta , Thomas George , Busheri Laleh , Reddy Asha , Kelkar Devaki , Dixit Santosh , Mannan Ashraf ul , Sabarinathan Radhakrishnan , Radhakrishna Selvi , Mishra Rupa , Koppiker Chaitanyanand B 
Published: June 2022

ABSTRACTPurposeBreast cancer is the most common cancer in Indian women with a high incidence of triple negative breast cancer (TNBC). The high TNBC prevalence (>25%) in India remains a challenge in clinical management. Association of germline BRCA1/2 mutations in TNBCs is well-established as a predisposing factor for hereditary breast cancer risk. These studies are however predominantly representative of western population. Therefore, we investigated germline profiles of multi-institutional cohort of TNBC patients in IndiaMethodsUsing a multi-gene NGS (next-generation sequencing) panel of 26 ACMG recommended genes associated with inherited cancers.ResultsIn our study cohort of 193 TNBC patients, we identified 57 pathogenic mutations of whichBRCA1(71.93%) andBRCA2(14.03%) were most commonly mutated. Additionally, 8 pathogenic mutations were identified in non-BRCA genes associated with the HR pathway. 10 novel mutations were identified in 3 genes namelyBRCA1,BRCA2andPALB2. Comparison of allele-frequency with the global databases like TCGA (The Cancer Genome Atlas), gnomAD and Genome Asia 100K indicated that the novel mutations were unique. Furthermore, we identified 48 variants of uncertain significance (VUS) (24.9%).ConclusionsOur study confirms the major proportion of mutations inBRCA1/2genes in TNBCs in India. Interestingly, a higher proportion of VUS were found in the non-BRCA genes compared to BRCA1/2 emphasizing the need for functional studies of the non-BRCA genes. Additionally, large scale studies are also warranted to elucidate the landscape of germline mutations relevant to the Indian population and their probable clinical implications.
Data Quality in health research: a systematic literature review
Authors: Bernardi Filipe Andrade , Alves Domingos , Crepaldi Nathalia Yukie , Yamada Diego Bettiol , Lima Vinícius Costa , Lopes Rijo Rui Pedro Charters 
Published: June 2022

AbstractDecision-making and strategies to improve service delivery need to be supported by reliable health data to generate consistent evidence on health status, so the data quality management process must ensure the reliability of the data collected. Thus, through an integrative literature review, the main objective of this work is to identify and evaluate digital health technology interventions designed to support the conduct of health research based on data quality. After analyzing and extracting the results of interest, 33 articles were included in the review. This transdisciplinarity may be reaching the threshold of significant growth and thus forcing the need for a metamorphosis of the area from focusing on the measurement and evaluation of data quality, today focused on content, to a direction focused on use and contextIn general, the main barriers reported in relation to the theme of research in the area of health data quality cite circumstances regarding a) use, b) systems and c) health services.. The resources presented can help guide medical decisions that do not only involve medical professionals, and indirectly contribute to avoiding decisions based on low-quality information that can put patients’ lives at risk
Assessing the effectiveness of newborn resuscitation training and skill retention program on neonatal outcomes in Madhesh Province, Nepal
Authors: Chalise Mala , Dhungana Ranjan , Visick Michael K , Clark Robert B 
Published: June 2022

AbstractBackgroundIntrapartum events leading to asphyxia at birth is one of the leading causes of neonatal morbidity and mortality in Nepal. In response to this, the Nepal Ministry of Health and Population adopted Helping Babies Breathe (HBB) as a tool to improve neonatal resuscitation. The effectiveness of HBB trainings in developing newborn resuscitation knowledge and skills of service providers have been well established. However, challenges remain in maintaining skills over time. Safa Sunaulo Nepal (SSN), with support from LDS Charities designed an initiative for scaling up newborn resuscitation training and maintaining skills over time. This paper reports on the implementation of SSN’s model of newborn resuscitation trainings and skill retention, and changes in perinatal outcomes that occurred during the program.MethodsThe program capacitated facility-based trainers for scale up and maintaining resuscitation skills in 20 facilities in Madhesh Province, Nepal. A single external mentor coached and assisted the facility-based trainers, provided general support, and monitored progress. Prospective outcome monitoring tracked changes in health metrics for a period of 14 months. To analyze changes over the time, the neonatal mortality, morbidity, and stillbirths at the baseline (first two months) of the program was compared with the endline (last two months) measures.ResultsData was gathered on neonatal health outcomes of 68,435 vaginal deliveries and 9,253 cesarean sections. Results indicate decreases in <24 hours neonatal deaths (p<0.001), intrapartum stillbirths (p<0.001), and number of sick newborns transferred from the maternity unit (p<0.001). During the program, facility-based trainers taught resuscitation skills to 231 medical personnel and supported skill retention.ConclusionsSSN’s model is a low-cost, evidence-based program focusing on facility-based trainers, who are mentored and supported to scale-up and sustain resuscitation skills over time. Findings from the report are suggestive that the model had a substantial influence on critical neonatal outcomes. Future programs focused on improving neonatal outcomes may benefit by incorporating program elements of SSN model.