Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased Visual Sensitivity and Occipital Activity in Patients With Hemianopia Following Vision Rehabilitation

Hemianopia, loss of vision in half of the visual field, results from damage to the visual pathway posterior to the optic chiasm. Despite negative effects on quality of life, few rehabilitation options are currently available. Recently, several long-term training programs have been developed that show visual improvement within the blind field, although little is known of the underlying neural changes. Here, we have investigated functional and structural changes in the brain associated with visual rehabilitation. Seven human participants with occipital lobe damage enrolled in a visual training program to distinguish which of two intervals contained a drifting Gabor patch presented within the blind field. Participants performed ∼25 min of training each day for 3–6 months and undertook psychophysical tests and a magnetic resonance imaging scan before and after training. A control group undertook psychophysical tests before and after an equivalent period without training. Participants who were not at ceiling on baseline tests showed on average 9.6% improvement in Gabor detection, 8.3% in detection of moving dots, and 9.9% improvement in direction discrimination after training. Importantly, psychophysical improvement only correlated with improvement in Humphrey perimetry in the trained region of the visual field. Whole-brain analysis showed an increased neural response to moving stimuli in the blind visual field in motion area V5/hMT. Using a region-of-interest approach, training had a significant effect on the blood oxygenation level-dependent signal compared with baseline. Moreover, baseline V5/hMT activity was correlated to the amount of improvement in visual sensitivity using psychophysical and perimetry tests. This study, identifying a critical role for V5/hMT in boosting visual function, may allow us to determine which patients may benefit most from training and design adjunct interventions to increase training effects. SIGNIFICANCE STATEMENT Homonymous visual field loss is a common consequence of brain injury and is estimated to affect more than 230,000 people in the United Kingdom. Despite its high prevalence and well-described impact on quality of life, treatments to improve visual sensitivity remain experimental, and deficits are considered permanent after 6 months. Our study shows that behavioral changes following vision rehabilitation are associated with enhanced visually-evoked occipital activity to stimuli in the blind visual field. Unlike previous behavioral studies, we observe clinical changes that are specific to the trained region of vision. This lends significant weight to such training paradigms and offers a mechanism by which visual function can be improved despite damage to the primary visual pathway.
Measuring Arsenic Speciation in Environmental Media: Sampling, Preservation, and Analysis

There is an extensive literature relating to As contents of various geological and biological media, driven in large part because of As-related diseases, which include for example, melanosis, leucomelanosis, keratosis, hyper-keratosis, oedema, gangrene, skin cancer and extensive liver damage. As an example, using the keywords “arsenic” and “environmental” in the academic search engine Scopus yields >12,300 references (title, abstract, and keywords). However, there is also increasing recognition that the toxicology of As is controlled by the form (speciation) of As (Scopus “Arsenic” and “speciation” yields >2900 references). It is commonly held that inorganic As(III) is the most toxic form, followed by arsenate (As(V)), with the various methylated forms generally having much less toxicity, although the epidemiology of the methylated forms has not been as well studied (e.g., Bacquart et al. 2010; Kobayashi 2010; Quazi et al. 2011; Whaley-Martin et al. 2013). However, the effect of inorganic speciation on human metabolism is debatable because As(V) is rapidly reduced after ingestion. Recent studies have shown that cellular biomethylation can result in the production of trivalent methylated As species, which can be more toxic than inorganic As forms (e.g., Styblo et al. 2000; Mass et al. 2001; Dopp et al. 2010; Rahman and Hassler 2014). For a recent review of As toxicology, see Mitchell (2014, this volume). Because in most terrestrial waters As(III) occurs as a neutral species (H3AsO3°), arsenite is more difficult to remove from solution in terms of water treatment, without first undergoing an oxidation step (e.g., Hu et al. 2012). There are a large variety of techniques for the measurement of total As and arsenic species, both in the field and in the laboratory. For the former, the main challenges are analytical time, complexity of sample treatment and …
Fibroblasts as confederates of the immune system

Fibroblastic stromal cells are as diverse, in origin and function, as the niches they fashion in the mammalian body. This cellular variety impacts the spectrum of responses elicited by the immune system. Fibroblast influence on the immune system keeps evolving our perspective on fibroblast roles and functions beyond just a passive structural part of organs. This review discusses the foundations of fibroblastic stromal‐immune crosstalk, under the scope of stromal heterogeneity as a basis for tissue‐specific tutoring of the immune system. Focusing on the skin as a relevant immunological organ, we detail the complex interactions between distinct fibroblast populations and immune cells that occur during homeostasis, injury repair, scarring, and disease. We further review the relevance of fibroblastic stromal cell heterogeneity and how this heterogeneity is central to regulate the immune system from its inception during embryonic development into adulthood.
METHODOLOGICAL ASPECTS OF USING A WEARABLE EYE-TRACKER TO SUPPORT DIAGNOSTIC CLINICAL EVALUATION OF PROLONGED DISORDERS OF CONSCIOUSNESS

Objective To evaluate the feasibility of using a wearable eye-tracker when assessing patients with pro-longed disorders of consciousness using the Coma Recovery Scale Revised (CRS-R), focusing on technical challenges. Design A methodological investigation with descriptive and analytical elements. Subjects Four patients with prolonged disorders of consciousness were recruited from the rehabilitation clinic of a regional rehabilitation unit. Methods A selection of subtests in the CRS-R were performed while recording eye movements with a wearable eye-tracker. Results No major adverse reactions were observed, suggesting likely patient acceptability. Calibration was not always possible. However, distinct eye movements were discernible from the recorded data even without calibration, and analysis of these produced results with the potential to support clinical assessment. Conclusion Eye tracking was feasible during clinical assessment for this patient group. Recording eye movement responses in these easily fatigued patients has the potential to add sensitivity for detection of conscious responses and to complement clinical examination. Further study is merited. Current hardware and software limitations can be overcome with manual data processing and analysis; however, significant developments in automating data processing will be required for broader clinical application. LAY ABSTRACT Some survivors of profound acquired brain injury develop a prolonged disorder of consciousness. Differentiation of the stage of prolonged disorders of consciousness is of relevance when planning rehabilitation and informing families. It currently relies largely on clinical assessment using standardized neurobehavioural rating scales. In the Coma Recovery Scale Revised (CRS-R) the patient is encouraged to perform tasks while the clinician observes. The patient’s responses may, however, be difficult to interpret due to impairments associated with the brain injury. The objective of this study was to develop eye-tracking as a supporting tool to CRS-R assessment of patients with prolonged disorders of consciousness. A selection of subtests in the CRS-R were performed while recording eye movements with a wearable eye-tracker. No major adverse reactions were observed, suggesting likely patient acceptability. Distinct eye movements were discernible from the recorded data, and analysis of these gave results with the potential to support clinical assessment. Further study is merited.
Clinical impact of lymphatic spread in patients with limited-stage upper aerodigestive tract NK/T cell lymphoma

Background We investigated whether distancemax, that is, the degree of distance between the upper aerodigestive tract (UAT) mass and the farthest pathologic lymph node, was significantly associated with survival in patients with limited-stage UAT natural killer/T cell lymphoma (NKTCL). Methods A total of 157 patients who received chemotherapy (CTx) with/without radiotherapy (RTx) were enrolled. Results In the survival analysis, an elevated lactate dehydrogenase level [progression-free survival (PFS) hazard ratio (HR), 2.948; 95% confidence interval (CI), 1.606‒5.404; P<0.001; overall survival (OS) HR, 2.619; 95% CI, 1.594‒4.822; P=0.003], short distancemax (PFS HR, 0.170; 95% CI, 0.071‒0.410; P<0.001; OS HR, 0.142; 95% CI, 0.050‒0.402; P< 0.001), and CTx combined with RTx (HR, 0.168; 95%CI, 0.079‒0.380; P<0.001; OS HR, 0.193; 95% CI, 0.087‒0.429; P<0.001) had an independent predictive value for PFS and OS. Conclusion The evaluation of the degree of lymphatic spread and local control by CTx combined with RTx is essential in patients with limited-stage UAT NKTCL.
AAPM Task Group 198 Report: An Implementation Guide for TG 142 Quality Assurance of Medical Accelerators.

The charges on this task group (TG) were as follows: (1) provide specific procedural guidelines for performing the tests recommended in TG 142; (2) provide estimate of the range of time, appropriate personnel, and qualifications necessary to complete the tests in TG 142; (3) provide sample daily, weekly, monthly, or annual quality assurance (QA) forms. Many of the guidelines in this report are drawn from the literature and are included in the references. When literature was not available, specific test methods reflect the experiences of the TG members (for example, a test method for door interlock is self-evident with no literature necessary). In other cases, the technology is so new that no literature for test methods was available. Given broad clinical adaptation of volumetric modulated arc therapy (VMAT), which is not a specific topic of TG 142, several tests and criteria specific to VMAT were added.
Associations between infection intensity categories and morbidity prevalence in school-age children are much stronger for Schistosoma haematobium than for S. mansoni

Background World Health Organization (WHO) guidelines for measuring global progress in schistosomiasis control classify individuals with Schistosoma spp. infections based on the concentration of excreted eggs. We assessed the associations between WHO infection intensity categories and morbidity prevalence for selected S. haematobium and S. mansoni morbidities in school-age children. Methodology A total of 22,488 children aged 6–15 years from monitoring and evaluation cohorts in Burkina Faso, Mali, Niger, Uganda, Tanzania, and Zambia from 2003–2008 were analyzed using Bayesian logistic regression. Models were utilized to evaluate associations between intensity categories and the prevalence of any urinary bladder lesion, any upper urinary tract lesion, microhematuria, and pain while urinating (for S. haematobium) and irregular hepatic ultrasound image pattern (C-F), enlarged portal vein, laboratory-confirmed diarrhea, and self-reported diarrhea (for S. mansoni) across participants with infection and morbidity data. Principal findings S. haematobium infection intensity categories possessed consistent morbidity prevalence across surveys for multiple morbidities and participants with light infections had elevated morbidity levels, compared to negative participants. Conversely, S. mansoni infection intensity categories lacked association with prevalence of the morbidity measures assessed. Conclusions/significance Current status infection intensity categories for S. haematobium were associated with morbidity levels in school-age children, suggesting urogenital schistosomiasis morbidity can be predicted by an individual’s intensity category. Conversely, S. mansoni infection intensity categories were not consistently indicative of childhood morbidity at baseline or during the first two years of a preventive chemotherapy control program.
Preliminary Characterization of NP339, a Novel Polyarginine Peptide with Broad Antifungal Activity

Fungi cause disease in nearly one billion individuals worldwide. Only three classes of antifungal agents are currently available in mainstream clinical use. ABSTRACT Fungi cause disease in nearly one billion individuals worldwide. Only three classes of antifungal agents are currently available in mainstream clinical use. Emerging and drug-resistant fungi, toxicity, and drug-drug interactions compromise their efficacy and applicability. Consequently, new and improved antifungal therapies are urgently needed. In response to that need, we have developed NP339, a 2-kDa polyarginine peptide that is active against pathogenic fungi from the genera Candida, Aspergillus, and Cryptococcus, as well as others. NP339 was designed based on endogenous cationic human defense peptides, which are constituents of the cornerstone of immune defense against pathogenic microbes. NP339 specifically targets the fungal cell membrane through a charge-charge-initiated membrane interaction and therefore possesses a differentiated safety and toxicity profile to existing antifungal classes. NP339 is rapidly fungicidal and does not elicit resistance in target fungi upon extensive passaging in vitro. Preliminary analyses in murine models indicate scope for therapeutic application of NP339 against a range of systemic and mucocutaneous fungal infections. Collectively, these data indicate that NP339 can be developed into a highly differentiated, first-in-class antifungal candidate for poorly served invasive and other serious fungal diseases.
Influence of phytoestrogens on endometrial thickness: a systematic review and meta-analysis

Abstract The objective of this systematic review was to evaluate the influence of the use of phytoestrogens on variations in endometrial thickness in postmenopausal women. Randomized controlled trials were searched in the following electronic databases until March 2020: MEDLINE, Embase, Cochrane Library, Web of Science and LILACS. We used the terms ‘phytoestrogens’ and ‘endometrium’ or ‘endometrial hyperplasia’ to search for relevant trials. The data were analyzed using RevMan 5.3 software. A total of 10 studies involving 1476 patients were included. The difference in endometrial thickness was evaluated in 10 studies, with a total of 805 participants in the phytoestrogen group and 761 in the control group. Such a difference was not significant between groups after 3 months (standardized mean difference [SMD] 0.00, 95% confidence interval [CI] − 0.37 to 0.37; I 2 = 63%), 6 months (SMD −0.30, 95% CI −0.79 to 0.19; I 2 = 70%), 12 months (SMD −0.02, 95% CI 0.22 to −0.18; I 2 = 0%) and 24 months (SMD –0.09, 95% CI −0.25, 0.08; I 2 = 0%) of use. Our meta-analysis shows no changes in endometrial thickness in women using phytoestrogens. Evidence is still uncertain owing to the presence of heterogeneity among the studies currently available, whose reported outcomes cover a period between 3 and 6 months.
Using naso- and oro-intestinal catheters in physiological research for intestinal delivery and sampling in vivo: practical and technical aspects to be considered.

ABSTRACT Intestinal catheters have been used for decades in human nutrition, physiology, pharmacokinetics, and gut microbiome research, facilitating the delivery of compounds directly into the intestinal lumen or the aspiration of intestinal fluids in human subjects. Such research provides insights about (local) dynamic metabolic and other intestinal luminal processes, but working with catheters might pose challenges to biomedical researchers and clinicians. Here, we provide an overview of practical and technical aspects of applying naso- and oro-intestinal catheters for delivery of compounds and sampling luminal fluids from the jejunum, ileum, and colon in vivo. The recent literature was extensively reviewed, and combined with experiences and insights we gained through our own clinical trials. We included 60 studies that involved a total of 720 healthy subjects and 42 patients. Most of the studies investigated multiple intestinal regions (24 studies), followed by studies investigating only the jejunum (21 studies), ileum (13 studies), or colon (2 studies). The ileum and colon used to be relatively inaccessible regions in vivo. Custom-made state-of-the-art catheters are available with numerous options for the design, such as multiple lumina, side holes, and inflatable balloons for catheter progression or isolation of intestinal segments. These allow for multiple controlled sampling and compound delivery options in different intestinal regions. Intestinal catheters were often used for delivery (23 studies), sampling (10 studies), or both (27 studies). Sampling speed decreased with increasing distance from the sampling syringe to the specific intestinal segment (i.e., speed highest in duodenum, lowest in ileum/colon). No serious adverse events were reported in the literature, and a dropout rate of around 10% was found for these types of studies. This review is highly relevant for researchers who are active in various research areas and want to expand their research with the use of intestinal catheters in humans in vivo.
Transactivation response DNA‐binding protein of 43 kDa proteinopathy and lysosomal abnormalities in spastic paraplegia type 11

Spastic paraplegia type 11 (SPG11) is the most common autosomal recessive hereditary spastic paraplegia with thinning of the corpus callosum. Spatacsin, a protein encoded by the SPG11 gene, is associated with autophagy. SPG11 patients show spastic paraplegia, intellectual disability, dementia, and parkinsonism. A previous neuropathological analysis of SPG11 cases reported neurodegeneration mimicking amyotrophic lateral sclerosis without transactivation response DNA‐binding protein of 43 kDa (TDP‐43) deposits and unique sequestosome 1 (SQSTM1)‐positive neuronal inclusions. We performed a neuropathological examination of two Japanese patients with complicated spastic paraplegia with thinning of the corpus callosum from different families, and one was genetically diagnosed as having SPG11. Both cases showed diffuse atrophy of the brain and spinal cord. Depigmentation of the substantia nigra was also observed. Immunohistochemistry revealed widespread distribution of areas showing TDP‐43 aggregation in the central nervous system. The TDP‐43 deposits in the thalamus and substantia nigra especially resembled skein‐like inclusions. Unique SQSTM1‐positive neuronal inclusions, as previously reported, were widespread in the whole central nervous system as well as the dorsal root ganglia. Double‐labeling immunofluorescence of the dorsal root ganglia revealed that the unique, large SQSTM1‐positive cytoplasmic inclusions of the ganglion cells were labeled with lysosome‐associated membrane protein 1 and lysosome‐associated membrane protein 2. This is the first report showing TDP‐43 pathology in SPG11. The common neuropathological findings of TDP‐43–positive inclusions in both the cases imply a causal connection between the TDP‐43 proteinopathy and autophagy dysfunction in SPG11.
Herd solutions from genetic evaluations can be used as a tool to rescale the expected expression of genetic potential in cattle.

The objective of this study was to determine whether response to selection for carcass weight (CW), conformation (CC) and fat (CF), and the association between heterosis and carcass performance varied by herd environment in cattle. Following edits, carcass information was available for 4,616,761 cattle, of which the majority were some crossbred combination of the following breeds: Angus, Aubrac, Belgian Blue, Blonde d'Aquitaine, Charolais, Hereford, Holstein-Friesian, Jersey, Limousin, Saler, Shorthorn and Simmental. Herd environment was defined separately for each carcass trait using herd solutions outputted from carcass trait genetic evaluations. A total of 3,859 herds were stratified, for each trait, into one of five strata based on their corresponding percentile herd solution rank, with the response to selection and the effect of heterosis then estimated within each stratum. The response in CW and CC from selection on the respective estimated breeding values (EBV) increased between the lowest (0.71 kg and 0.89 CC score increase per unit increase in the respective EBV) and highest (0.99 kg and 1.25 CC score increase per unit increase in the respective EBV) corresponding herd stratum. The response in CF from selection on CF EBV, however, reduced between the lowest and highest CF herd stratum (respective increases of 0.93 and 0.83 CF scores per unit increase in CF EBV). In addition, the effect of a unit increase in heterosis coefficient on CW, CC and CF also varied by herd stratum. Furthermore, results (i.e. the area under relative operating characteristic curves) from the present study demonstrated that the response to selection and heterosis effects estimated for the different herd stratum can be used, along with EBVs and the herd solutions themselves, to improve the accuracy of phenotypic predictions. Results from the present study could help producers to make more informed breeding decisions that are bespoke to their herd.
Threat imminence modulates neural gain in attention and motor relevant brain circuits in humans.

Different levels of threat imminence elicit distinct computational strategies reflecting how the organism interacts with its environment in order to guarantee survival. Thereby, parasympathetically driven orienting and inhibition of on-going behavior in post-encounter situations and defense reactions in circa-strike conditions associated with sympathetically driven action preparation are typically observed across species. Here, we show that healthy humans are characterized by markedly variable individual orienting or defense response tendencies as indexed by differential heart rate (HR) changes during the passive viewing of unpleasant pictures. Critically, these HR response tendencies predict neural gain modulations in cortical attention and preparatory motor circuits as measured by neuromagnetic steady-state visual evoked fields (ssVEFs) and induced beta-band (19-30 Hz) desynchronization, respectively. Decelerative HR orienting responses were associated with increased ssVEF power in the parietal cortex and reduced beta-band desynchronization in pre-motor and motor areas. However, accelerative HR defense response tendencies covaried with reduced ssVEF power in the parietal cortex and lower beta-band desynchronization in cortical motor circuits. These results show that neural gain in attention- and motor-relevant brain areas is modulated by HR indexed threat imminence during the passive viewing of unpleasant pictures. The observed mutual ssVEF and beta-band power modulations in attention and motor brain circuits support the idea of two prevalent response tendencies characterized by orienting and motor inhibition or reduced stimulus processing and action initiation tendencies at different perceived threat imminence levels.