bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning for risk stratification in kidney disease
Authors: Gulamali Faris F. , Sawant Ashwin S. , Nadkarni Girish N. 
Published: August 2022

Purpose of review
Risk stratification for chronic kidney is becoming increasingly important as a clinical tool for both treatment and prevention measures. The goal of this review is to identify how machine learning tools contribute and facilitate risk stratification in the clinical setting.

Recent findings
The two key machine learning paradigms to predictively stratify kidney disease risk are genomics-based and electronic health record based approaches. These methods can provide both quantitative information such as relative risk and qualitative information such as characterizing risk by subphenotype.

Summary
The four key methods to stratify chronic kidney disease risk are genomics, multiomics, supervised and unsupervised machine learning methods. Polygenic risk scores utilize whole genome sequencing data to generate an individual's relative risk compared with the population. Multiomic methods integrate information from multiple biomarkers to generate trajectories and prognostic different outcomes. Supervised machine learning methods can directly utilize the growing compendia of electronic health records such as laboratory results and notes to generate direct risk predictions, while unsupervised machine learning methods can cluster individuals with chronic kidney disease into subphenotypes with differing approaches to care.
Lack of a coherent theory limits the diagnostic and prognostic value of the (central) auditory processing disorder: a theoretical and clinical perspective
Authors: Cacace Anthony T. , Enayati Zakaria 
Published: August 2022

Purpose of reviewTo consider pertinent issues towards developing a coherent theory of the auditory processing disorder (APD). By identifying the conceptual and methodological shortcomings that have thwarted development in this area for decades, we propose solutions to achieve a veridical endpoint to advance the field.Recent findingsConcerted efforts in the theoretical, experimental, and clinical domains have focused on validating the APD by demonstrating the “modality specificity” of the deficit. The importance of this conceptual framework is the delineation of auditory-perceptual dysfunctions from more generalized “supramodal” deficits, like those related to attention, memory, and language. Because contemporary schemata have limited the assessment of APD to auditory tasks alone (unimodaltesting), functional dissociations cannot be established, indeterminate diagnoses are problematic, and progress remains unduly constrained. The use of matched tasks in multiple sensory modalities is advocated as a diagnostic imperative to remedy this deficiency.SummaryThemes covered by this review include the need to develop a coherent theory of APD, to identify and limit factors which confound a valid diagnosis, and to validate the diagnosis by demonstrating the “modality specificity” of the deficit. Without an obligatory theoretical designation, the APD will remain as an obscure and controversial entity, limited to indeterminate test results and misdiagnoses.
Cochlear implantation in systemic autoimmune disease
Authors: Goh Xueying , Muzaffar Jameel , Bance Manohar 
Published: August 2022

Purpose of review
Autoimmune inner ear disease (AIED) is a rare, but likely underrecognized cause of hearing loss. However, hearing loss is common in systemic autoimmune disease and it is important for the clinician to be familiar with the spectrum of disease. In this article, we will review the developments in diagnosis and management of AIED, with a focus on the outcomes and potential pitfalls of cochlear implantation.

Recent findings
Hearing loss in AIED tends to be progressive and bilateral, but up to 40% can present as sudden hearing loss and one-third can present unilaterally. HSP-70 serology may help with diagnosis and may predict steroid response. Cochlear implantation provides excellent hearing and quality of life outcomes in patients deafened by AIED. Intracochlear fibrosis/ossification is found intraoperatively in the majority (54%) of patients undergoing cochlear implantation. A large percentage (32%) of patients has fluctuating impedances postimplantation, which may interfere with implant performance and mapping.

Summary
Diagnosis of AIED is largely clinical, and a strong index of suspicion is required. Multidisciplinary care is crucial for optimal management. Cochlear implant outcomes are generally excellent, but the clinician needs to be cognizant of the pitfalls of encountering intracochlear fibrosis intraoperatively and likelihood of implant performance fluctuation related to ongoing inflammation in the cochlea.
The remaining obstacles for a totally implantable cochlear implant
Authors: Trudel Mathieu , Morris David P. 
Published: August 2022

Purpose of the reviewFor years, the development of a totally implantable cochlear implant (TICI) has faced several technical challenges hindering any prototypes from reaching full commercialization. This article aims to review the necessary specifications for a viable TICI. An overview of the remaining challenges when designing TICIs will be provided, focusing on energy supply and implantable microphones.Recent findingsThe literature review highlights how research efforts to generate sufficient power to supply a fully implantable CI could take advantage of microelectromechanical systems (MEMS)-based energy harvesters incorporating piezoelectric materials. Using one of the various energy sources in the vicinity of the temporal bone would allow the development of a self-sufficient implant, overcoming the limitations of electrochemical batteries. Middle ear implantable microphones could also use similar fabrication techniques and transduction mechanisms to meet the sensor requirements for a TICI.SummaryRecent breakthroughs in power supply using MEMS-based energy harvesting technologies and piezoelectric implantable microphones may make TICIs become a more practical reality in the foreseeable future. Once available, TICIs will have major impact on our patients’ quality of life and may help to make hearing rehabilitation a more appealing option to a greater proportion of those who fulfill our candidacy criteria.
Anterior cervical spine surgery and dysphagia
Authors: Nachalon Yuval 
Published: August 2022

Purpose of review
The purpose of this review is to summarize current evidence regarding dysphagia in anterior cervical spine surgeries (ACSS) and to present recent advances in evaluation and surgical technique.

Recent findings
Various risk factors for dysphagia have been identified, and they include female sex, smoking history, prior surgery and cervical lordotic angle. EAT-10 is a validated tool for the assessment of individuals with dysphagia post-ACSS. Local intraoperative corticosteroid application significantly reduced the incidence and magnitude of dysphagia in four out of five studies that were reviewed. Individuals who had undergone cervical disc replacement (CDR) and revision surgery by a zero-profile anchored spacer (ROI-C) device experienced less dysphagia than those who had anterior cervical discectomy with fusion (ACDF). Videofluoroscopic swallow study (VFSS) after ACSS demonstrated pharyngeal weakness and increased posterior pharyngeal wall thickness, while no other abnormality was found.

Summary
Different technique variations can reduce dysphagia severity in individuals undergoing ACSS. Surgeons are encouraged to continue performing randomized control studies to assist in choosing the most favourable technique for the patient.
The association between self-efficacy and completion of first-line treatment among newly referred patients with lung cancer
Authors: Kjaer Trille K. , Hansen Nina H. G. , Levinsen Anne Katrine G. , Carlsen Signe , Mellemgaard Anders , Oksen Marianne S. , Andersen Ingelise , Dalton Susanne O. 
Published: August 2022

Abstract

Background:
Clinical factors have an impact on the planning and completion of lung cancer treatment, but it is not well documented how psychological factors such as self-efficacy, that is, a person's belief in his or her own ability to respond to and control challenges in life, might affect completion of lung cancer treatment. We explored the association between general self-efficacy and completion of planned first-line treatment among newly referred patients with lung cancer.

Methods:
A total of 137 patients with lung cancer newly referred to the Oncology Department at Herlev University Hospital, Denmark, participated in this study. Data were prospectively collected through questionnaires and medical records. The Generalized Self-Efficacy Scale was used to assess self-efficacy at the time of diagnosis. Logistic regression models were used to analyze the association between self-efficacy and completion of planned first-line treatment with adjustment for age, sex, education, marital status, disease stage, and comorbidity.

Results:
Patients with high self-efficacy had significantly higher odds for completing first-line treatment (odds ratio 1.10; 95% confidence interval: 1.03–1.19) after adjustments.

Conclusions:
Patients who reported having higher self-efficacy were more likely to complete first-line treatment than patients with lower self-efficacy. This finding suggests that taking patients' psychological resources into account when planning for treatment may have potential to improve treatment for vulnerable patients with lung cancer. However, more studies are needed to confirm our findings.
Anatomy and Sonographic Examination for Lateral Epicondylitis: EURO-MUSCULUS/USPRM* Approach
Authors: Ricci Vincenzo , Cocco Giulio , Mezian Kamal , Chang Ke-Vin , Naňka Ondřej , Tamborrini Giorgio , Kara Murat , Özçakar Levent 
Published: August 2022

ABSTRACT

Objective
To define a standardized comprehensive sonographic approach for evaluating the different histo-anatomical compartments of the lateral elbow.

Design
Using high-frequency US probes, we tried to match the anatomical features of the lateral elbow and its different sonographic patterns in patients with the diagnosis of lateral epicondylitis. Moreover, high-sensitive color/power Doppler assessments have also been performed to evaluate the microcirculation.

Results
Modern US equipment appears to provide an extremely detailed sonographic assessment of the different anatomical layers located in the lateral compartment of the elbow. Moreover, high-sensitive color/power Doppler imaging allows for clear visualization of the perfusion patterns in pathological conditions.

Conclusion
In clinical practice, high-frequency B-mode and high-sensitive color/power Doppler imaging can be integrated with the clinical findings to better define the pain generator(s) for optimizing the management of patients with lateral epicondylitis.
Understanding the effects of Universal Test and Treat on longitudinal HIV care continuum outcomes among South African youth: a retrospective cohort study
Authors: Filiatreau Lindsey M. , Edwards Jessie K. , Masilela Nkosinathi , Gómez-Olivé F. Xavier , Haberland Nicole , Pence Brian W. , Maselko Joanna , Muessig Kathryn E. , Kabudula Chodziwadziwa Whiteson , Dufour Mi-Suk Kang , Lippman Sheri A. , Kahn Kathleen , Pettifor Audrey 
Published: August 2022

AbstractIntroductionLittle is known about when youth living with HIV (YLHIV) are most susceptible to disengagement from HIV care. The longitudinal HIV care continuum is an underutilized tool that can provide a holistic understanding of population-level HIV care trajectories and be used to compare treatment outcomes across groups. We aimed to explore effects of the Universal Test and Treat policy (UTT) on longitudinal care outcomes among South African youth living with HIV (YLHIV) and identify temporally precise opportunities for re-engaging this priority population.MethodsUsing medical record and census data, we conducted a retrospective cohort study among youth aged 18-24 newly diagnosed with HIV between August 2015 and December 2018 in nine health care facilities in rural South Africa. We used weighted Fine and Grey sub-distribution proportional hazards models to characterize longitudinal care continuum outcomes in the population overall and stratified by treatment era of diagnosis. We estimated the proportion of individuals in each stage of the continuum over time and the mean time spent in each stage in the first year following diagnosis. Estimates for the two groups were compared using differences (diagnosis pre-UTT=referent).ResultsA total of 420 YLHIV were included. By the end of the first year following diagnosis, just 23% of individuals had no 90-or-more-day lapse in care and were virally suppressed. Those diagnosed in the UTT era spent less time as ART-naïve (mean difference=-19.3 days; 95% CI: - 27.7, -10.9) and more time virally suppressed (mean difference=17.7; 95% CI: 1.0, 34.4) compared to those diagnosed pre-UTT adoption. Most individuals who were diagnosed in the UTT era and experienced a 90-or-more-day lapse in care disengaged between diagnosis and linkage to care or ART initiation and viral suppression.ConclusionsImplementation of UTT yielded modest improvements in time spent on ART and virally suppressed among South African YLHIV. However, meeting UNAIDS’ 95-95-95 targets remains a challenge in this priority population. Retention in care and re-engagement interventions that can be implemented between diagnosis and linkage to care (e.g., longitudinal counseling following diagnosis) or ART initiation and viral suppression may be particularly important to improving treatment outcomes among South African YLHIV.
Pupil-linked phasic arousal relates to the reduction of response inhibition: inferences from a simultaneous pupillometry and EEG-fMRI study
Authors: Hong Linbi , He Hengda , Sajda Paul 
Published: August 2022

AbstractAttention reorienting is a critical cognitive function which drives how we respond to novel and unexpected stimuli. In recent years, arousal has been linked to attention reorienting. The timing and spatial organization of the interactions between the arousal and reorienting systems, however, remain only partially revealed. Here, we investigate the dynamics between the two systems through simultaneous recordings of pupillometry, EEG, and fMRI of healthy human subjects while they performed an auditory target detection task. We used pupil diameter and activity in the noradrenergic locus coeruleus to infer arousal, and found these measures linked to distinct cortical activity at various temporal stages of the reorienting response. Specifically, our results provide the first demonstration in humans of how phasic pupil-linked arousal relates to the reduction of response inhibition, an inference which otherwise would remain hidden without the help of simultaneous multi-modal acquisitions.
Multiplex genome engineering in Clostridium beijerinckii NCIMB 8052 using CRISPR-Cas12a
Authors: Patinios Constantinos , de Vries Stijn T. , Diallo Mamou , Lanza Lucrezia , Verbrugge Pepijn L. J. V. Q. , López-Contreras Ana M. , van der Oost John , Weusthuis Ruud A. , Kengen Servé W. M. 
Published: August 2022

AbstractClostridium species are re-emerging as biotechnological workhorses for industrial acetone-butanol-ethanol production. This re-emergence is largely due to advances in fermentation technologies but also due to advances in genome engineering and re-programming of the native metabolism. Several genome engineering techniques have been developed including the development of several CRISPR-Cas tools. Here, we expanded the CRISPR-Cas toolbox and developed a CRISPR-Cas12a genome engineering tool in Clostridium beijerinckii NCIMB 8052. By controlling the expression of FnCas12a with the strict xylose-inducible promoter, we achieved efficient (25-100%) single-gene knockout of five C. beijerinckii NCIMB 8052 genes (Spo0A, Upp, Cbei_1291, Cbei_3238, Cbei_3832). Moreover, we achieved multiplex genome engineering by simultaneously knocking out the Spo0A and Upp genes in a single step with an efficiency of 18%. Finally, we showed that the spacer sequence and position in the CRISPR array can affect the editing efficiency outcome.
Effects of Aging on Cortical Representations of Continuous Speech
Authors: Karunathilake I.M Dushyanthi , Dunlap Jason L. , Perera Janani , Presacco Alessandro , Decruy Lien , Anderson Samira , Kuchinsky Stefanie E. , Simon Jonathan Z. 
Published: August 2022

AbstractUnderstanding speech in a noisy environment is crucial in day-to-day interactions, and yet becomes more challenging with age, even for healthy aging. Age-related changes in the neural mechanisms that enable speech-in-noise listening have been investigated previously; however, the extent to which age affects the timing and fidelity of encoding of target and interfering speech streams are not well understood. Using magnetoencephalography (MEG), we investigated how continuous speech is represented in auditory cortex in the presence of interfering speech, in younger and older adults. Cortical representations were obtained from neural responses that time-locked to the speech envelopes using speech envelope reconstruction and temporal response functions (TRFs). TRFs showed three prominent peaks corresponding to auditory cortical processing stages: early (∼50 ms), middle (∼100 ms) and late (∼200 ms). Older adults showed exaggerated speech envelope representations compared to younger adults. Temporal analysis revealed both that the age-related exaggeration starts as early as ∼50 ms, and that older adults needed a substantially longer integration time window to achieve their better reconstruction of the speech envelope. As expected, with increased speech masking, envelope reconstruction for the attended talker decreased and all three TRF peaks were delayed, with aging contributing additionally to the reduction. Interestingly, for older adults the late peak was delayed, suggesting that this late peak may receive contributions from multiple sources. Together these results suggest that there are several mechanisms at play compensating for age-related temporal processing deficits at several stages, but which are not able to fully reestablish unimpaired speech perception.NEW & NOTEWORTHYWe observed age-related changes in cortical temporal processing of continuous speech that may be related to older adults’ difficulty understanding speech in noise. These changes occur in both timing and strength of the speech representations at different cortical processing stages, and depend on both noise condition and selective attention. Critically, their dependency on noise condition changes dramatically among the early, middle, and late cortical processing stages, underscoring how aging differentially affects these stages.
Evaluation of salinity tolerance of lowland rice genotypes at the reproductive stage
Authors: Rafaliarivony Safidimanjato , Ranarijaona Hery Lisy Tiana , Rasoafalimanana Mbolarinosy , Radanielina Tendro , Wissuwa Matthias 
Published: August 2022

AbstractSalinity is an abiotic stress considered as the most widespread soil problem next to drought in rice growing areas of the world. To facilitate agricultural production on salt-affected soil, water and soil management is the most common practice, but this approach is increasingly problematic because water is becoming scarce. Therefore, developing tolerant varieties would the best solution to this problem. The present study evaluated salinity tolerance of 72 lowland rice genotypes at the reproductive stage. Experiments were conducted in irrigated fields at Marovoay, Madagascar, under low and moderately high salinity with electric conductivities of 2 dSm-1 and 4 dSm-1, respectively. A subsequent validation experiment was conducted in a pot experiment at three levels of salinity corresponding to 0, 4 and 8 dSm-1. Plant height, panicle number, panicle length, panicle fertility, spikelet fertility, straw weight and grain yield were measured together with a visual score of salt injury. Field salinity strongly reduced panicle number and spikelet fertility, reducing grain yield to less than 10 g m-2 in sensitive genotypes compared to more than 60 g m-2 in tolerant genotypes. The field experiment classified 20% of genotypes as tolerant, 50% as intermediate and 30% as sensitive to salinity. Four genotypes IR55179, MTM13_1, MTM13_3, MTM13_5, were re-confirmed as highly tolerant in the pot experiment. Higher spikelet and panicle fertility in tolerant genotypes contributed to their superior grain yield under salinity stress whereas these traits were particularly reduced in the sensitive local varieties. Genotypes with tolerance to salinity at the reproductive stage identified here could be used as donors to improve grain yield of local sensitive varieties, possibly using spikelet and panicle fertility as selection criteria for screening breeding lines at the reproductive stage.
Data-Driven Predictions of Potential Leishmania Vectors in Latin America
Authors: Vadmal Gowri M. , Glidden Caroline K. , Han Barbara A. , Carvalho Bruno , Castellanos Adrian A. , Mordecai Erin A. 
Published: August 2022

AbstractThe incidence of vector-borne diseases is rising as deforestation, climate change, and globalization bring humans in contact with arthropods that can transmit pathogens. In particular, incidence of American Cutaneous Leishmaniasis (ACL), a parasitic disease transmitted by sandflies, is increasing as previously intact habitats are cleared for agriculture and urban areas, potentially bringing people into contact with vectors and reservoir hosts. Previous evidence has identified dozens of sandfly species that have been infected with and/or transmit Leishmania parasites. However, there is an incomplete understanding of which sandfly species transmit the parasite, complicating efforts to limit disease spread. Here, we apply machine learning models (boosted regression trees) to leverage biological and geographical traits of known sandfly vectors to predict potential vectors. Additionally, we generate trait profiles of confirmed vectors and identify important factors in transmission. Our model performed well with an average out of sample accuracy of 86%. The models predict that synanthropic sandflies living in areas with greater canopy height, less human modification, and within an optimal range of rainfall are more likely to be Leishmania vectors. We also observed that generalist sandflies that are able to inhabit many different ecoregions are more likely to transmit the parasite. Our results suggest that Psychodopygus amazonensis and Nyssomia antunesi are unidentified potential vectors, and should be the focus of sampling and research efforts. Overall, we found that our machine learning approach provides valuable information for Leishmania surveillance and management in an otherwise complex and data sparse system.Author SummaryAmerican Cutaneous Leishmaniasis (ACL) is a neglected parasitic disease transmitted by sandflies in Latin America. There is an incomplete understanding of which sandfly species transmit the parasite, complicating efforts to limit disease spread. In this study, the authors created a database of sandfly traits, then used predictive models to determine important factors in disease transmission and how different climate and environmental variables affect ACL transmission. The models suggest that transmission occurs at the interface between domestic habitats and well-preserved forests. The authors also generate predictions of which sandflies might be transmitting the parasite that are not known vectors at the time, specifically Psychodopygus amazonensis and Nyssomia antunesi. This new knowledge can lead to a better understanding of the system of transmission, and can point to possible hotspots of the disease. The analysis can also help direct researchers to areas of interest for sampling studies, as well as specific sandflies to focus their effort on.