bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spinal cord stimulation for gait impairment in Parkinson Disease: scoping review and mechanistic considerations
Authors: Singh Omesh , Carvalho Diego Z , Espay Alberto J , Benarroch Eduardo E , Grewal Sanjeet S , Pagani-Estévez Gabriel L 
Published: October 2023

Abstract

Objective
Advanced Parkinson's Disease (PD) is associated with Parkinson’s Disease gait impairment (PDg), which increases the risk for falls and is often treatment-refractory. Subthalamic nucleus (STN) and globus pallidus pars interna (GPi) deep brain stimulation (DBS) often fails to improve axial symptoms like PDg. Spinal cord stimulation (SCS) has been suggested to improve PDg. SCS may benefit PDg by disrupting pathologic beta-oscillations and hypersynchrony in cortico-striatal-thalamic circuits to override excessive inhibition of brainstem locomotor regions. SCS may potentially improve locomotion by acting at any of these levels, either alone or in combination.

Methods
We conducted a comprehensive literature search and scoping review, identifying 106 patients in whom SCS was evaluated for PDg.

Results
Among the identified patients, 63% carried a pain diagnosis. Overall, the most common stimulation location was thoracic (78%), most commonly T9-T10. Burst (sub-perception) was the most common stimulation modality (59%). Prior treatment with DBS was used in 25%. Motor outcomes were assessed by the Unified Parkinson Disease Rating Scale (UPDRS) III-motor, UPDRS, the Timed Up and Go (TUG), and/or 10-/20-meter walking tests.
Among these patients, 95 (90%) had PDg amelioration and improved motor outcomes.

Conclusions
Despite small sample sizes, patient heterogeneity, and unblinded evaluations complicating interpretations of efficacy and safety, SCS may be beneficial for at least a subset of PDg. Further research is required to clarify the role of SCS for PDg and the patients most suitable to benefit from this intervention.
The Significance of Bell's Palsy That Presents as Monocranial Versus Polycranial Neuropathy: A Case Series and Systematic Literature Review
Authors: Ziv Oren , Hazout Chen , Goldberg Nitzan , Tavdi Alex , Zholkovsky Ariel , Kordeluk Sofia , El-Saied Sabri , Dinur Anat Bahat , Ben-Zion Joshua , Muhanna Nidal , Ungar Omer J. 
Published: October 2023

Purpose
To investigate the effect of Bell's palsy (BP) presenting as polycranial neuropathy (PCN) compared with BP caused by isolated facial nerve (CNVII).

Methods
We carried out a retrospective cohort study of the medical records of all consecutive patients who were diagnosed with BP at a single tertiary referral center between 2010 and 2017. Included were patients 18 years or older who were clinically diagnosed with BP and completed 7 days of systemic steroidal treatment and at least 6 months of follow-up. The patients were divided into two groups according to whether the BP derived from a monocranial neuropathy or a PCN. Demographics and BP severity and outcome were compared between these groups. A systematic literature review using Medline via “PubMed,” “Embase,” and “Web of Science” was conducted.

Results
In total, 321 patients with BP were enrolled. The median (interquartile range) age at presentation was 44 (33–60) years. Sex distribution showed male predominance of 57.6% (n = 185) versus 42.4% (n = 136), and 21.2% (n = 68) had PCN. The most concomitantly affected cranial nerve (CN) was the trigeminal (CNV; n = 32, 47%), followed by the glossopharyngeal nerve (CNIX; n = 14, 21%) and the audiovestibular nerve (CNVIII; n = 10, 15%). Age, House-Brackmann score on presentation, and diabetes mellitus (DM) were independent predictors for PCN etiology (p = 0.001, p = 0.034, and p < 0.001, respectively). Each increase in 1 year of age was associated with additional odds ratio (95% confidence interval) of 0.97 (0.95–0.99) for PCN. The odds ratio (95% confidence interval) associated with DM was 8.19 (4.02–16.70). Our systematic literature review identified 1,440 patients with the PCN type of BP. The most commonly affected CN was the trigeminus (25–48%), followed by the glossopharyngeal and audiovestibular nerves (2–19% and 0–43%, respectively).

Conclusion
The severity of facial weakness on initial presentation among PCN patients was significantly higher compared with the monocranial neuropathy–type BP patients. The authors believe that the significant association and prevalence rate ratio between DM and PCN warrant that a patient presenting with PCN undergo screening for DM.
Evaluation of Stroke Risk Following COVID-19 mRNA Bivalent Vaccines Among U.S. Adults Aged ≥65 Years
Authors: Lu Yun , Matuska Kathryn , Nadimpalli Gita , Ma Yuxin , Duma Nathan , Zhang Henry , Chiang Yiyun , Lyu Hai , Chillarige Yoganand , Kelman Jeffrey , Forshee Richard , Anderson Steven A. 
Published: October 2023

ABSTRACTIn January 2023, the United States Food and Drug Administration and the Centers for Disease Control and Prevention noted a safety concern for ischemic stroke in adults ≥65 years receiving the BNT162b2; WT/OMI BA.4/BA.5 COVID-19 bivalent vaccine. This self-controlled case series analysis evaluated stroke risk among Medicare fee-for-service beneficiaries aged ≥65 years receiving: 1) a Pfizer-BioNTech (BNT162b2; WT/OMI BA.4/BA.5) or Moderna (mRNA-1273.222) COVID-19 bivalent vaccine, 2) high-dose/adjuvanted influenza vaccines, and 3) concomitant COVID-19 bivalent vaccines and influenza vaccines, from August 31 to November 6, 2022.The primary analysis did not find elevated stroke risk following COVID-19 bivalent vaccines. In the age subgroup analyses, only the ≥85 year age group had a risk of NHS (Incident Rate Ratio (IRR)=1.36, 95% CI 1.09 – 1.69 [1-21 days]) and NHS/TIA (IRR=1.28, 95% CI 1.08 – 1.52 [1-21 days]) with BNT162b2 Bivalent WT/OMI BA.4/BA.5. Among beneficiaries receiving a concomitant COVID-19 bivalent vaccine and a high-dose/adjuvanted influenza vaccine, an increased risk was observed for NHS (IRR=1.20, 95% CI 1.01 – 1.42 [22-42 days]) with BNT162b2 Bivalent WT/OMI BA.4/BA.5 and for TIA (IRR=1.35, 95% CI 1.06 – 1.74 [1-21 days]) with mRNA-1273.222.Results of the secondary analyses showed a small increased risk of NHS following high-dose or adjuvanted influenza vaccines (IRR=1.09, 95% CI 1.02 – 1.17 [22-42 days]).
Migration routes and wintering sites of the Aquatic WarblersAcrocephalus paludicolabreeding in Lithuania and North Belarus
Authors: Flade Martin , Lisovski Simeon , Eigirdas Vytauras , Giessing Benedikt , Jiguet Fréderic , Keišs Oskars , Nemtchinov Maxim 
Published: October 2023

AbstractFor the effective protection of the globally threatened Aquatic Warbler in its entire range, knowledge of the migration and wintering areas as well as their current conservation status is of great importance. The question on where the different breeding population overwinter where (connectivity) equally important. This is also essential when new breeding populations are re-established in restored breeding sites through translocation from other, distant areas, as recently performed in Lithuania. From previous geolocator studies in central Ukraine and south-western Belarus, as well as from ringing data, it was known that these populations overwinter in Mali (Inner Niger Delta IND) and southern Mauritania. In addition, at least some birds of the NE-Polish breeding population overwinter in the Senegal delta (ring recovery). In 2018 and 2019, the migratory routes, stopover and wintering sites of two breeding populations at the north-western distribution range border in N-Belarus (29 males) and Lithuania (31 males) were investigated using light-level geolocators. All 19 recovered data loggers recorded almost complete annual cycles from mid-July to at least early April. Migration and overwintering sites of both populations did not differ significantly. Most (16 out of 19) birds also spent the winter in the Inner Niger Delta and surrounding wetlands within and around Mali. Only one bird from Belarus hiberbated in the Senegal Delta. One of the Lithuanian birds overwintered in northern Burkina Faso, another northern Nigeria. In addition, important details about the course of migration routes, timing and resting areas could be obtained. For example, the outstanding importance of Morocco and northern Algeria as resting areas on spring migration became obvious. The investigations applying geolocators resulted in a very complex and differentiated picture of the migration and stopover pattern of adult male Aquatic Warblers.
Maternal high-fat diet affects the contents of eggs and causes abnormal development in the medaka fish
Authors: Inoue Yusuke , Fukushima Manatsu , Hirasawa Go , Furukawa Fumiya , Takeda Hiroyuki , Umatani Chie 
Published: October 2023

AbstractMaternal nutritional status can affect development and metabolic phenotypes of their progeny in animals. The effects of maternal diet are thought to be mediated mainly by changes inside oocytes such as organelles, maternal RNAs, and metabolites. However, to what extent each factor contributes to offspring phenotypes remains uncertain, especially in viviparous mammalian systems, where factors other than oocytes, such as placenta and milk, need to be considered. Here, using the medaka fish as an oviparous vertebrate model, we examined whether maternal high-fat diet (mHFD) feeding affects offspring development, and what kind of changes occur in the contents of mature eggs. We found that mHFD caused the high frequency of embryonic deformities of offspring, accompanied by downregulation of transcription- and translation-related genes and zygotic transcripts at the blastula stage. Transcriptomic and metabolomic analyses of mature eggs suggested decreased catabolism of amino acids and glycogen, moderate upregulation of endoplasmic reticulum stress-related genes, and elevated lipid levels in mHFD eggs. Furthermore, HFD females showed upregulation of follicle-stimulating hormone, a higher incidence of oocyte atresia and downregulation of egg protein genes in the liver. These data suggested that attenuated amino acid catabolism triggered by decreased yolk protein load/processing, as well as elevated lipid levels inside eggs, are the prime candidates that account for the higher incidence of embryonic deformities in mHFD offspring. Our study presents a comprehensive data on the changes inside eggs in mHFD model of non-mammalian vertebrates, and provides insights into the mechanisms of parental nutritional effects on their offspring.
Relative Homoplasy Index: A New Cross-comparable Metric for Quantifying Homoplasy in Discrete Character Datasets
Authors: Steell Elizabeth M. , Hsiang Allison Y. , Field Daniel J. 
Published: October 2023

AbstractHomoplasy is among the main hinderances to phylogenetic inference. However, investigating patterns of homoplasy can also improve our understanding of macroevolution, for instance by revealing evolutionary constraints on morphology, or highlighting convergent form-function relationships. Several methods have been proposed to quantify the extent of homoplasy in discrete character matrices, but the consistency index (CI) and retention index (RI) have remained the most widely used for decades, with little recent scrutiny of their function. Here, we test the performance of CI and RI using simulated and empirical datasets and investigate patterns of homoplasy with different matrix scenarios. In addition, we describe and test a new scaled metric, the relative homoplasy index (RHI), implemented in the R statistical environment. The results suggest that, unlike the RI, the CI does not constitute a direct measure of homoplasy. However, the RI consistently underestimates the extent of homoplasy in phylogenetic character-taxon matrices, particularly in datasets characterised by high levels of homoplasy. By contrast, RHI—the newly proposed metric—outperforms both methods in sensitivity to homoplasy levels, and is scaled between zero and one for comparison of values between different datasets. Using both simulated and empirical phylogenetic datasets, we show that relative levels of homoplasy remain constant with the addition of novel characters, and, in contrast to earlier work, decrease with the addition of taxa. Our results help illuminate the inherent properties of homoplasy in cladistic matrices, opening new potential avenues of research for investigating patterns of homoplasy in macroevolutionary studies.
Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
Authors: Mikelov Artem , Nefediev George , Tashkeev Alexander , Rodriguez Oscar L. , Ortmans Diego A. , Skatova Valeriia , Izraelson Mark , Davydov Alexey , Poslavsky Stanislav , Rahmouni Souad , Watson Corey T. , Chudakov Dmitriy , Boyd Scott D. , Bolotin Dmitry 
Published: October 2023

Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), has been shown to be of critical importance for immune responses to pathogens and vaccines. In recent years, B cell and T cell receptor repertoire sequencing (Rep-Seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci in different populations. Here we present a novel algorithm for extra-sensitive and specific variable (V) and joining (J) gene allele inference and genotyping allowing reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput genotyping and novel allele discovery from a wide variety of existing datasets. The developed algorithm is a part of the MiXCR software (https://mixcr.com) and can be incorporated into any pipeline utilizing upstream processing with MiXCR.We demonstrate the accuracy of this approach using Rep-Seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) Rep-Seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA; TRB) Rep-Seq dataset, representing 134 individuals. This allowed us to assess the genetic diversity of genes within the IGH, TRA and TRB loci in different populations and demonstrate the connection between antibody repertoire gene usage and the number of allelic variants present in the population. Finally we established a database of allelic variants of V and J genes inferred from Rep-Seq data and their population frequencies with free public access athttps://vdj.online.
Alkaline and loess grasslands with contrasting richness and biomass patterns are not separated on the CSR strategy spectrum
Authors: McIntosh-Buday Andrea , Sonkoly Judit , Molnár Attila , Szél-Tóth Katalin , Törő-Szijgyártó Viktória , Madar Szilvia , Károlyi Evelin , Díaz Cando Patricia Elizabeth , Kovacsics-Vári Gergely , Tóthmérész Béla , Török Péter 
Published: October 2023

AbstractStudying the relationship between biodiversity patterns and processes in vegetation has been at the centre of interest in vegetation ecology for several decades. By studying the biomass of loess and alkaline grasslands along a water and salinity gradient, we aimed to analyse species diversity and CSR functional type patterns. We aimed to test the following hypotheses: i) The biomass and species richness scores and the species composition are significantly different between the sampled grassland community types. ii) The sampled communities are well separated based on the CSR strategy spectrum. iii) The amount of green biomass and litter are positively correlated with competitiveness and negatively with stress tolerance. The biomass and species richness scores and the species composition of the sampled communities along the sampled gradients were significantly different; the highest species richness, evenness and Shannon diversity values were found in loess grasslands. The highest level of litter accumulation was found in alkaline meadows. The communities were well separated in the ordinations but surprisingly, calculation of coordinates for CSR strategy types have not shown clear separation of the grassland community types. Based on the results we can conclude that the current CSR classification is too robust to delineate grassland communities in alkaline landscapes which are markedly different in composition. We point out that the CSR classification is based on the magnitude of stress, and it is not able to differentiate between the various forms of stress which might be responsible for the marked compositional differences. Therefore, developing an index focusing specifically on the functional characterisation of stressed communities and able to differentiate between different forms of stress (e.g., water and/or salinity stress) would be highly beneficial for future studies.
Scale dependency of taxonomic and functional diversity in old-growth and secondary loess steppic grasslands
Authors: Török Péter , Teleki Balázs , Erdős László , McIntosh-Buday Andrea , Ruprecht Eszter , Tóthmérész Béla 
Published: October 2023

AbstractWidespread campaigns on forest restoration and various tree planting actions lower the awareness of the importance of grasslands for carbon sequestration or biodiversity conservation. Even lower attention is given to the conservation of biodiversity and ecosystem functioning in remnants of ancient, so called old-growth grasslands. Old-growth grasslands in general harbour high biodiversity and even small patches of these can act as important refuges for many plant and animal species in urbanised or agriculture driven landscapes. Spontaneous succession of grassland is frequently viewed as a cost-effective tool for grassland restoration, but its applicability is strongly dependent on many local to landscape-scale factors and the recovery often slow. Thus, for the assessment of the effectiveness of spontaneous succession as a restoration tool, it is essential to compare the species diversity and functional attributes of old-growth and secondary grasslands. We studied the taxonomic and functional diversity in thirteen loess steppic grasslands (8 old-growth and 5 secondary) using differently sized plots ranging from 0.01 to 100m2. Our results indicated that there are remarkable differences in taxonomic and functional diversity between old-growth grasslands and secondary ones. We also point out that during secondary succession there is a likely functional saturation of the species assembly in the first few decades of recovery, and while patterns and structure of secondary grasslands became quite similar to those of old-growth grasslands, the species richness and diversity remains still much lower. Old-growth grasslands support considerable plant diversity, and species composition is slow to recover if destroyed for agricultural land use. This underlines the priority of protecting existing old-growth grassland remnants over restoration actions and the recovery of secondary grasslands.
Mapping the topography of spatial gene expression with interpretable deep learning
Authors: Chitra Uthsav , Arnold Brian J. , Sarkar Hirak , Ma Cong , Lopez-Darwin Sereno , Sanno Kohei , Raphael Benjamin J. 
Published: October 2023

AbstractSpatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of this data complicates the analysis of spatial gene expression patterns such as gene expression gradients. We address these issues by deriving atopographic mapof a tissue slice—analogous to a map of elevation in a landscape—using a novel quantity called theisodepth. Contours of constant isodepth enclose spatial domains with distinct cell type composition, while gradients of the isodepth indicate spatial directions of maximum change in gene expression. We develop GASTON, an unsupervised and interpretable deep learning algorithm that simultaneously learns the isodepth, spatial gene expression gradients, and piecewise linear functions of the isodepth that model both continuous gradients and discontinuous spatial variation in the expression of individual genes. We validate GASTON by showing that it accurately identifies spatial domains and marker genes across several biological systems. In SRT data from the brain, GASTON reveals gradients of neuronal differentiation and firing, and in SRT data from a tumor sample, GASTON infers gradients of metabolic activity and epithelial-mesenchymal transition (EMT)-related gene expression in the tumor microenvironment.
Cardiac-sympathetic contractility and neural alpha-band power: cross-modal collaboration during approach-avoidance conflict
Authors: Dundon Neil M. , Stuber Alexander , Bullock Tom , Garcia Javier O. , Babenko Viktoriya , Rizor Elizabeth , Yang Dengxian , Giesbrecht Barry , Grafton Scott T. 
Published: October 2023

SummaryAs evidence mounts that the cardiac-sympathetic system reacts to challenging cognitive settings, we ask if these responses are passive companions or if they are instead fundamentally intertwined with cognitive function. Healthy human participants performed an approach-avoidance paradigm, trading off monetary reward for painful electric shock, while we recorded simultaneous neural and cardiac signals. Participants were reward-sensitive, but also experienced approach-avoidance “conflict” when the subjective appeal of the reward was near equivalent to the revulsion of the cost. Drift-diffusion model parameters revealed that participants managed conflict in part by integrating larger volumes of evidence into choices (wider decision boundaries). Late alpha-band (neural) dynamics suggested that widening decision boundaries served to combat reward-sensitivity and spread attention more fairly to all dimensions of available information. Independently, wider boundaries were also associated with cardiac “contractility” (an index of sympathetically-mediated positive inotropy). We also saw evidence of conflict-specific collaboration between the neural and cardiac-sympathetic signals. Specific to states of conflict, the alignment (i.e., product) of alpha dynamics and contractility were associated with a further widening of the boundary, independent of either signal’s singular influence. Cross-trial coherence analyses provided additional support for a direct role of cardiac-sympathetics in nurturing fair assessment of information streams during conflict by disrupting the prepotent reward signals. We conclude that cardiac-sympathetic activity is not a mere companion, rather it is a critical component collaborating with cognitive processes to combat reward-sensitivity during the approach-avoidance conflict.