Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of Y in regulatory T lymphocytes in the tumor micro-environment of primary colorectal cancers and liver metastases

Male sex is a risk factor for colorectal cancer (CRC) with higher illness burden and earlier onset. Thus, we hypothesized that loss of chromosome Y (LOY) in the tumor micro-environment (TME) might be involved in oncogenesis. Previous studies show that LOY in circulating leukocytes of aging men was associated with shorter survival and non-hematological cancer, as well as higher LOY in CD4+ T-lymphocytes in men with prostate cancer vs. controls. However, nothing is known about LOY in leukocytes infiltrating TME and we address this aspect here. We studied frequency and functional effects of LOY in blood, TME and nontumorous tissue. Regulatory T-lymphocytes (Tregs) in TME had the highest frequency of LOY-cells (22%) in comparison to CD4+ T-lymphocytes and cytotoxic CD8+ T-lymphocytes. Using scRNA-seq LOY was also linked to higher expression of PDCD1, TIGIT and IKZF2 in Tregs. PDCD1 and TIGIT encode immune checkpoint receptors involved in the regulation of Tregs function. Our study sets the direction for further functional research regarding a probable role of LOY in intensifying features related to the suppressive phenotype of Tregs in TME and consequently a possible influence on immunotherapy response in CRC patients.
A Novel Autosomal Dominant Childhood-Onset Disorder Associated with Pathogenic Variants in VCP

Valosin-containing protein (VCP) is an AAA+ ATPase that plays critical roles in multiple ubiquitin-dependent cellular processes. Dominant pathogenic variants in VCP are associated with adult-onset multisystem proteinopathy (MSP) that presents with myopathy, bone disease, dementia, and/or motor neuron disease. Through GeneMatcher, we identified 13 unrelated individuals who carry novel heterozygous VCP variants (12 de novo, 1 inherited) associated with a childhood-onset disorder characterized by developmental delay, intellectual disability, hypotonia, and macrocephaly. Trio exome sequencing or multigene panel identified nine missense variants, two in-frame deletions, one frameshift, and one splicing variant. We performed in vitro functional studies and in silico modelling to investigate the impact of these variants on protein function. In contrast to MSP variants, most missense variants had decreased ATPase activity, and one caused hyperactivation. Other variants were predicted to cause haploinsufficiency, suggesting a loss-of-function mechanism. This is the first description of VCP-related neurodevelopmental disease presenting in childhood.
Spatiotemporal dynamics of hippocampal-cortical networks underlying the unique phenomenological properties of trauma-related intrusive memories

Trauma-related intrusive memories (TR-IMs) possess unique phenomenological properties that contribute to adverse post-traumatic outcomes, positioning them as critical intervention targets. However, transdiagnostic treatments for TR-IMs are scarce, as their underlying mechanisms have been investigated separate from their unique phenomenological properties. Extant models of more general episodic memory highlight dynamic hippocampal-cortical interactions that vary along the anterior-posterior axis of the hippocampus (HPC) to support different cognitive-affective and sensory-perceptual features of memory. Extending this work into the unique properties of TR-IMs, we conducted a study of eighty-four trauma-exposed adults who completed daily ecological momentary assessments of TR-IM properties followed by resting-state functional magnetic resonance imaging (rs-fMRI). Spatiotemporal dynamics of anterior and posterior hippocampal (a/pHPC)-cortical networks were assessed using co-activation pattern analysis to investigate their associations with different properties of TR-IMs. Emotional intensity of TR-IMs was inversely associated with the frequency and persistence of an aHPC-default mode network co-activation pattern. Conversely, sensory features of TR-IMs were associated with more frequent co-activation of the HPC with sensory cortices and the ventral attention network, and the reliving of TR-IMs in the here-and-now was associated with more persistent co-activation of the pHPC and the visual cortex. Notably, no associations were found between HPC-cortical network dynamics and conventional symptom measures, including TR-IM frequency or retrospective recall, underscoring the utility of ecological assessments of memory properties in identifying the neural substrates of memory properties. These findings provide novel mechanistic insights into the unique features of TR-IMs that are critical for the development of individualized, transdiagnostic treatments for this pervasive, difficult-to-treat symptom.
Avalanche photodiodes beyond 1.65 μm

There are many applications where the ability to detect optical signals in the 1.65 - 3 μm wavelength range would be of considerable interest. In this paper we discuss two technologies that offer considerable promise for high speed, high sensitivity detection in this region utilising avalanche gain. InGaAs/GaAsSb Type II superlattices as the absorption region and InAlAs as the multiplication region can be combined to form a separate absorption and multiplication (SAM) avalanche photodiode (APD), all grown lattice matched on InP substrates. Detection at room temperature up to 2.4 μm can be readily achieved as can gains in excess of 40. InAs homojunction p-i-n diodes are capable of detecting light with wavelengths > 3 μm, even at 77 K. Although controlling the surface leakage current is a major challenge in mesa devices of InAs, gains in excess of 40 have also been obtained in these devices at room temperature. InAs is also the only III-V semiconductor material that appears to show excess noise-free avalanche gain when electrons are used to initiate the avalanche multiplication. We will discuss recent developments in these two material systems to date and the current state of the technology.
Electron density and temperature in a diffuse nanosecond pulse discharge in air at atmospheric pressure

This work presents the first experimental results on the electron properties of a nanosecond diffuse fast ionisation wave generated in synthetic dry air at atmospheric pressure under very strong overvoltage. Both density and mean temperature of electrons are investigated by incoherent Thomson scattering. The electron density is also derived from the Stark broadening of oxygen lines resolved by optical emission spectroscopy. The extreme voltages applied question some common hypothesis of the diagnostics implemented. The solutions adopted and the remaining limitations are discussed in the paper. Each diagnostic covers a specific region of interest within the discharge and they show good agreement in conditions where they overlap. It is shown that most of the volume of the pin-to-plane discharge is quite representative of a quasi-steady state glow discharge dominated by the emission of the first and second positive systems of nitrogen. Once its propagation completed within the first two nanoseconds and until the end of the 10 ns pulse, it is characterized by rather homogeneous properties close to the axis. The electron density is of the order of 1015 cm−3 and the mean temperature is about 3 eV within the whole air gap. About 6 ns after the start of the discharge from the pin, a sub-millimetric region of strong ionization develops at the pin, which is consistent with the observation of a continuum of emission spreading from the UV to the near-IR spectral range. Within this part of the discharge, the electron density reaches values greater than 1017 cm−3 with an ionization degree higher than 1%. The radiative recombination of nitrogen ions N2 + and the three-body recombination of N+ with a large number of electrons could help to explain the continuum.
Theoretical investigation of substitutionally doped symmetrical finite phenine nanotubes

Ab initio density functional theory calculations were performed to investigate the substitutional doping of boron and nitrogen in symmetrical phenine nanotubes. It was found that the doped structures are energetically favorable and can be grown experimentally. Furthermore, we investigated how electronic and magnetic properties of these nanotubes change in the presence of electron-rich (nitrogen) and electron-deficient (boron) impurities, and found that doping in these tubes resulted in a non-magnetic structure. The doping changes the electronic structure of the tube by reducing the energy gap and the reduction value is sensitive to the nanotube diameter and impurity type. The gap corresponding to the nitrogen doped tubes is in the range of 2.38 eV-2.64 eV, whereas for boron doped tubes, the value lies in 1.91 eV to 2.11 eV, respectively. Moreover, the nitrogen doped phenine nanotubes tend to be n-type semi-conductor. The doped phenine nanotube molecules with a high stability and tunable electronic properties may offer several interesting applications in nano-electronics.
SAR evaluation in models of an adult and a child for magnetic field from wireless power transfer systems at 6.78 MHz

One of the promising applications for wireless power transfer (WPT) systems is to charge consumer electronics devices. Resonant-type wireless chargers operate at the frequency of 6.78 MHz and may be mounted inside office desks and table tops. In this frequency band, the specific absorption rate (SAR) averaged over 10 g of tissue is an essential factor to be evaluated for human protection from radio-frequency near-field exposure. Detailed analysis of a peak value of 10 g averaged SAR for WPT system with multiple receivers has not been conducted so far. In this study, we compare the peak values of 10 g averaged SAR for the magnetic field leaked from WPT systems with a transmitting coil coupled with a single- or double receiving coil. From computational results, we observed a marginal enhancement of the SAR for the exposure scenario with double-receiving coils. The SAR in the child was smaller than that in the adult because of the difference in the magnetic flux density passing through the human body model. When comparing the SARs in the standing and sitting postures, the former SAR was observed to be 20–30% greater than the latter.
A numerical method to calculate screening current-dependent self and mutual inductances of REBCO coils

The screening current and its relaxation cause the variation of the self- and mutual inductances of REBCO coils—REBCO is one of the high-temperature superconductors. However, most studies of coil voltage analysis on a REBCO magnet, a stack of coils, have reported simulation results assuming invariant self- and mutual inductances so far. Although the conventional assumption of invariant inductances is still acceptable for fundamental coil voltage analyses, it can cause misleading conclusions due to inductive voltage errors when a precise coil voltage analysis is demanded. Hence, here we report a numerical method to calculate screening-current-dependent self- and mutual inductances of REBCO coils for advanced studies based on a lumped-circuit analysis model. In this work, we aim to investigate the inductance variation due to the screening current with a case study and discuss its effects on the coil voltage. We assume that there is a stack of 12 REBCO single-pancake coils. No transverse current in each coil is considered for simplicity. A numerical simulation of the current density in the magnet is performed, and then the inductances are calculated by considering the spatially non-uniform current density due to the screening current. From this case study, we confirm that the self- and mutual inductances are changed by up to 110% and 30% each. It is also confirmed that the discrepancy is notable at the beginning of the charge while marginal at the end. Finally, we discuss the effect of inductance variation on the quench voltage analysis.
Correlates of the Post-Stroke cognitive impairment among patients with first-ever stroke admitted at tertiary hospitals in Dodoma, Tanzania: a prospective longitudinal study

Introduction: Stroke patients develop cognitive impairment that, significantly impacting their quality of life, their families, and the community as a whole, but they are not given attention. This study aims to determine the prevalence and predictors of post-stroke cognitive impairment (PSCI) among adult stroke patients admitted to a tertiary hospital in Dodoma, Tanzania. Methodology: A prospective longitudinal study was conducted at tertiary hospitals in the Dodoma region, central Tanzania. A sample size of 158 participants with the first stroke confirmed by CT/MRI brain aged [≥] 18 years met the criteria. At baseline, social-demographic, cardiovascular risks and stroke characteristics were acquired and then at 30 days, participants were evaluated for depression and apathy. Descriptive statistics were summarised as continuous data reported as Mean (SD) or Median (IQR), and categorical data were summarised using proportions and frequencies. Univariate and multivariable logistic regression analysis were computed to determine predictors of PSCI Results: Of 158 participants, the mean age was 58.7 years, 57.6% were female, and 80.4% of participants met the criteria for post-stroke cognitive impairment. After multivariable logistic regression, left hemisphere stroke (AOR: 5.798, CI: 1.030 - 32.623, p = 0.046), a unit cm3 increase in infarct volume (AOR: 1.064, 95% CI: 1.018 - 1.113, p = 0.007), and apathy symptoms (AOR: 12.259, CI: 1.112 - 89.173, p = 0.041) had a significant association with PSCI. Conclusion: The study showed a high prevalence of PSCI; profiling at-risk stroke survivors in a timely intervention may improve their prognosis. Future studies in the area would inform future interventions and policies.
Reaching those at risk: Active case detection of leprosy and contact tracing at Kokosa, a hot spot district in Ethiopia

Introduction Leprosy is a chronic mycobacterial disease of public health importance. It is one of the leading causes of permanent physical disability. The prevalence of leprosy in Ethiopia has remained stagnant over the last decades. The aim of the study was to identify new leprosy cases and trace household contacts at risk of developing leprosy by active case detection. The study area was Kokosa district, West Arsi zone, Oromia region, Ethiopia. Method A prospective longitudinal study was conducted from June 2016-September 2018 at Kokosa district. Ethical approvals were obtained from all relevant institutions. Health extension workers screened households by house-to-house visits. Blood samples were collected and the level of anti-PGL-I IgM measured at two-time points. Results More than 183,000 people living in Kokosa district were screened. Dermatologists and clinical nurses with special training on leprosy confirmed the new cases, and their household contacts were included in the study. Of the 91 new cases diagnosed and started treatment, 71 were recruited into our study. Sixty-two percent were males and 80.3% were multibacillary cases. A family history of leprosy was found in 29.6% of the patients with cohabitation ranging from 10 to 30 years. Eight new leprosy cases were diagnosed among the 308 household contacts and put on multi-drug therapy. The New Case Detection Rate increased from 28.3/100,000 to 48.3/100,000 between 2015/2016 and 2016/2017. Seventy one percent of leprosy patients and 81% of the household contacts’ level of anti-PGL-I IgM decreased after treatment. In conclusion,the results of the study showed the importance of active case detection and household contact tracing. It enhances early case finding, and promotes early treatment, thereby interrupting transmission and preventing potential disability from leprosy.
Sleep Disturbance and Severe Hydrocephalus in a Normally Behaving Wistar Rat With Traumatic Brain Injury

We report on a case study of a Wistar rat that was investigated in detail because it exhibited no N3 sleep in electroencephalography (EEG) after lateral fluid-percussion injury (FPI)-induced traumatic brain injury (TBI). The rat (#112) belonged to a cohort of 28 adult Wistar rats exposed to lateral FPI. Rats were monitored by continuous video EEG for 30 days to follow-up on the evolution of sleep disturbances. The beam walking test was used to measure post-TBI functional recovery. Severity of the cortical lesion area, total brain volume, and cortical volume were measured from histological brain sections. Rat #112 had a normal body and skull appearance. Its baseline body weight did not differ from that of the rest of the cohort. At baseline, rat #112 crossed the beam in 6.3 sec (score range for the rest of the cohort, 4.7–44.3) and showed no evident slipping of the paws, scoring a 5.3 (score range for the rest of cohort, 4.3–6.0). On day 30 post-TBI, however, rat #112 was the only rat with a score of 0 on the beam. Histological analysis at 30 days post-TBI revealed a small 0.6-mm2 post-TBI lesion in the somatosensory cortex (lesion size range for the rest of the cohort, 1.2–10.9). The brain volume of rat #112 was 2-fold larger than the mean volume of the rest of the cohort (1592 vs. 758 mm3), the ventricles were remarkably enlarged, and the layered cerebral cortex was very thin. Analysis of the sleep EEG revealed that rat #112 had rapid eye movement sleep and wakefulness, but no N3 sleep, during the 72-h EEG epoch analyzed. This case report demonstrates that brain abnormalities presumably unrelated to the impact-induced cortical lesion, such as presumed pre-existing hydrocephalus, may worsen TBI-induced behavioral and electrographical outcome measures and complicate the assessment of the cause of the abnormalities.
Pituitary Metastases From Differentiated Thyroid Cancers: A Systematic Review

Background Pituitary metastasis (PM) from differentiated thyroid cancer (DTC) is extremely rare and may adversely affect outcomes. We aimed to assess the characteristics and outcomes of patients with PM from DTC. Methods We systematically reviewed the literature on publications on PM and the different DTC histologic types (papillary, follicular, and Hurthle cell cancers). Three databases (PubMed, Embase, and Scopus) were searched for articles published from 1967 to 2022. Survival time was estimated as the period from the first treatment of PM to the time of death or last follow-up. Results Twenty-five articles comprising 27 cases that met the eligibility criteria were identified using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The median age of the patients was 60 years (23 - 86). A preponderance of females (66.7%) with PM most commonly reported papillary thyroid cancer (55.6%). This was followed by follicular thyroid cancer (37.0%) and Hurthle cell cancer (7.4%). The most common presentations were headache, nausea, and vomiting, with visual symptoms in 44.4%. Diabetes insipidus was an infrequent finding (7.4%). The median time from diagnosis or first treatment of DTC to the diagnosis of PM was 3 years (0 - 25). The most common endocrine abnormality was hyperprolactinemia (63.2%), while the most frequently deficient hormone was luteinizing hormone (50%). The most common treatment modality for PM was a combination of radiotherapy and surgery with or without radio-iodine. At the end of the follow-up, 30% of the patients died. Only 33.3% of the patients achieved complete resolution of symptoms. The overall median survival time was 12 months (3 - 108). There was a moderate inverse correlation between the age of patients and survival, which was, however, not statistically significant (rs = -0.45, P = 0.103). Conclusion PM from DTC is extremely rare, and Hurtle cell cancer appears to be the least associated with PM. Diabetes insipidus is a rare initial manifestation of PM from DTC. Complete resolution of symptoms is less likely to be achieved in PM from DTC. Older age may confer an increased survival tendency, probably due to more intracranial space volume in older people compared to the younger population. Larger studies are needed to examine the relationship between age and survival in PM from DTC. Also, more observational data are required to determine the predictors of survival and compare the efficacy of the different treatment modalities in patients with PM from DTC.
Survival rates in the world's southernmost forest bird community

Abstract The Magellanic sub‐Antarctic Forest is home to the world's southernmost avian community and is the only Southern Hemisphere analogue to Northern Hemisphere temperate forests at this latitude. This region is considered among the few remaining pristine areas of the world, and shifts in environmental conditions are predominantly driven by climate variability. Thus, understanding climate‐driven demographic processes is critical for addressing conservation issues in this system under future climate change scenarios. Here, we describe annual survival patterns and their association with climate variables using a 20‐year mark–recapture data set of five forest bird species in the Cape Horn Biosphere Reserve. We develop a multispecies hierarchical survival model to jointly explore age‐dependent survival probabilities at the community and species levels in a group of five forest passerines. At the community level, we assess the association of migratory behavior and body size with survival, and at the species level, we investigate the influence of local and regional climatic variables on temporal variations of survival. We found a positive effect of precipitation and a negative effect of El Niño Southern Oscillation on juvenile survival in the white‐crested Elaenia and a consistent but uncertain negative effect of temperature on survival in juveniles and 80% of adults. We found only a weak association of climate variables with survival across species in the community and no temporal trends in survival for any of the species in either age class, highlighting apparent stability in these high austral latitude forests. Finally, our findings provide an important resource of survival probabilities, a necessary input for assessing potential impacts of global climate change in this unique region of the world.