Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on genetic variability, correlation and path analysis in lettuce (Lactuca sativa L.) under protected conditions

Twenty-eight genotypes of lettuce including check cultivars viz., Simpson Black Seeded and Great Lakes were grown in a RCBD with three replications during Rabi 2011-12 and 2012-13 at Vegetable Experimental Research Farm, Nauni, Solan H.P. to estimate the parameters of genetic variability, correlation and path analysis undernaturally ventilated polyhouse. Analysis of variance showed highly significant differences among genotypes for all the characters under study. Variability revealed that phenotypic co-efficient of variation (PCV) in general were higher than the corresponding genotypic co-efficient of variation (GCV) for all the characters. High co-efficient of variability were found for heading percentage (37.00% and 36.01%), incidence of sclerotinia rot (63.49% and 61.475%), gray mould (90.13% and 88.08%) and yield per plot (39.55% and 33.09%) indicated wider range of variation and offer better scope for improvement through selection. High heritability estimates coupled with moderate genetic gain were observed for yield and other horticultural traits. Correlation study indicated that yield per plot was positively correlated with gross and net head weight, seed germination, seed vigour index-I & II, 1000-seeds weight and also showed maximum direct effects towards yield per plot. The path co-efficient analysis revealed that net head weight has maximum positive direct effect on yield per plot followed by gross head weight, days to marketable maturity, seed germination, 1000-seeds weight, head shape index and incidence of sclerotinia rot. While, negative direct effect of number of non-wrapper leaves and incidence of gray mould was observed on yield. The new multicoloured cultivars indigenous and exotic mostly procured from CGN, Netherlands , identified for commercial cultivation under protected conditions in the mid hills of North Western Himalayas, may act as a substitute to the old cultivars with good quality and higher yielding potential.
Photoreceptor Degeneration in Pro23His Transgenic Rats (Line 3) Involves Autophagic and Necroptotic Mechanisms

Photoreceptor death contributes to 50% of irreversible vision loss in the western world. Pro23His (P23H) transgenic albino rat strains are widely used models for the most common rhodopsin gene mutation associated with the autosomal dominant form of retinitis pigmentosa. However, the mechanism(s) by which photoreceptor death occurs are not well understood and were the principal aim of this study. We first used electroretinogram recording and optical coherence tomography to confirm the time course of functional and structural loss. Electroretinogram analyses revealed significantly decreased rod photoreceptor (a-wave), bipolar cell (b-wave) and amacrine cell responses (oscillatory potentials) from P30 onward. The cone-mediated b-wave was also decreased from P30. TUNEL analysis showed extensive cell death at P18, with continued labeling detected until P30. Focused gene expression arrays indicated activation of, apoptosis, autophagy and necroptosis in whole retina from P14-18. However, analysis of mitochondrial permeability changes (ΔΨm) using JC-1 dye, combined with immunofluorescence markers for caspase-dependent (cleaved caspase-3) and caspase-independent (AIF) cell death pathways, indicated mitochondrial-mediated cell death was not a major contributor to photoreceptor death. By contrast, reverse-phase protein array data combined with RIPK3 and phospho-MLKL immunofluorescence indicated widespread necroptosis as the predominant mechanism of photoreceptor death. These findings highlight the complexity of mechanisms involved in photoreceptor death in the Pro23His rat model of degeneration and suggest therapies that target necroptosis should be considered for their potential to reduce photoreceptor death.
Layer 2/3 Pyramidal Neurons of the Mouse Granular Retrosplenial Cortex and Their Innervation by Cortico-Cortical Axons

The retrosplenial cortex forms part of the cingulate cortex and is involved in memory and navigation. It is ventral region, the granular retrosplenial cortex, or GRSC is characterized by the presence, of small pyramidal neurons with a distinctive late-spiking (LS) firing pattern in layer 2/3. Using in vitro brain slices of the mouse GRSC we have studied the electrophysiological properties and synaptic responses of these LS neurons, comparing them with neighboring non-LS pyramidal neurons. LS and non-LS neurons showed different responses during cortical propagation of epileptiform discharges. All non-LS neurons generated large supra-threshold excitatory responses that generated bursts of action potentials. Contrastingly, the LS neurons showed small, and invariably subthreshold excitatory synaptic potentials. Although both types of pyramidal neurons were readily intermingled in the GRSC, we observed differences in their innervation by cortico-cortical axons. The application of glutamate to activate cortical neurons evoked synaptic responses in LS neurons only when applied at less than 250 μm, while in non-LS neurons we found synaptic responses when glutamate was applied at larger distances. Analysis of the synaptic responses evoked by long-range cortico-cortical axons (with the origin at 1200 μm from the recorded neurons or in the contralateral hemisphere) confirmed that non-LS neurons were strongly innervated by these axons, while they evoked only small responses or no response at all in the LS neurons (contralateral stimulation, non-LS: 194.0 ± 196.63 pA, n = 22; LS: 51.91 ± 35.26 pA, n = 10; p = 0.004). The excitatory/inhibitory balance was similar in both types of pyramidal neurons, but the latency of the EPSCs evoked by long-range cortico-cortical axons was longer in LS neurons (contralateral stimulation non-LS: 8.13 ± 1.23 ms, n = 17; LS: 10.76 ± 1.58 ms, n = 7; p = 0.004) suggesting a disynaptic mechanism. Our findings highlight the differential cortico-cortical axonal innervation of LS and non-LS pyramidal neurons, and that the two types of neurons are incorporated in different cortico-cortical neuronal circuits. This strongly suggests that the functional organization of the dorsal part of the GRSC is based on independent cortico-cortical circuits (among other elements).
Machine Learning Classification Identifies Cerebellar Contributions to Early and Moderate Cognitive Decline in Alzheimer’s Disease

Alzheimer’s disease (AD) is one of the most common forms of dementia, marked by progressively degrading cognitive function. Although cerebellar changes occur throughout AD progression, its involvement and predictive contribution in its earliest stages, as well as gray or white matter components involved, remains unclear. We used MRI machine learning-based classification to assess the contribution of two tissue components [volume fraction myelin (VFM), and gray matter (GM) volume] within the whole brain, the neocortex, the whole cerebellum as well as its anterior and posterior parts and their predictive contribution to the first two stages of AD and typically aging controls. While classification accuracy increased with AD stages, VFM was the best predictor for all early stages of dementia when compared with typically aging controls. However, we document overall higher cerebellar prediction accuracy when compared to the whole brain with distinct structural signatures of higher anterior cerebellar contribution to mild cognitive impairment (MCI) and higher posterior cerebellar contribution to mild/moderate stages of AD for each tissue property. Based on these different cerebellar profiles and their unique contribution to early disease stages, we propose a refined model of cerebellar contribution to early AD development.
IS Reappraisal and Technology Adaptation Behaviors

Employees have to adapt to newly implemented information systems (IS) because they are often perceived as radical changes or disruptions. To understand such adaptation behavior, IS research suggests that employees first appraise the new IS and second perform technology adaptive behaviors. However, while the psychology literature indicates that adaptation is a continuous process unfolding over time, previous IS literature treats adaptation towards IS implementation as a rather singular, noniterative process. As firms continue to implement IS, an understanding of reappraisal and the influence of technology adaptation behavior is vital to ensure successful implementations. Therefore, the present paper investigates reappraisal and the influences of four different technology adaptation behaviors. We conducted a longitudinal study and used hierarchical linear modeling (HLM) to validate our research model. The findings reveal that employees reappraise the newly implemented IS over time regarding perceived opportunity, threat, and controllability and demonstrate that technology adaption behaviors influence such reappraisal. One specific finding is that employees might get into positive or negative reappraisal loops. We thereby contribute to research by extending the adaptation behavior literature and add a new piece of the puzzle to understand how employees adapt towards newly implemented IS over time.
Alterations in Degree Centrality and Functional Connectivity in Parkinson’s Disease Patients With Freezing of Gait: A Resting-State Functional Magnetic Resonance Imaging Study

Objective Freezing of gait (FOG) is a common disabling motor symptom in Parkinson’s disease (PD), but the potential pathogenic mechanisms are still unclear. Methods A total of 22 patients with PD with FOG (PD-FOG), 28 patients with PD without FOG (PD-nFOG), and 33 healthy controls (HCs) were recruited in this study. Degree centrality (DC)—a graph theory-based measurement of global connectivity at the voxel level by measuring the number of instantaneous functional connections between one region and the rest of the brain—can map brain hubs with high sensitivity, specificity, and reproducibility. DC was used to explore alterations in the centrality of PD-FOG correlated with brain node levels. PD-FOG cognitive network dysfunction was further revealed via a seed-based functional connectivity (FC) analysis. In addition, correlation analyses were carried out between clinical symptoms and acquired connectivity measurement. Results Compared to the PD-nFOG group, the PD-FOG group showed remarkably increased DC values in the right middle frontal gyrus (RMFG). There were no significant differences in other gray matter regions. Importantly, the clinical severity of FOG was related to the mean DC values in the RMFG. This brain region served as a seed in secondary seed-based FC analysis, and we further found FC changes in the right precuneus, right inferior frontal gyrus, right superior frontal gyrus (SFG), and cerebellum. Conclusion Increased RMFG activity and FC network alterations in the middle frontal cortex with the precuneus, inferior, and SFG, and the cerebellum may have great potential in brain dysfunction in PD with FOG.
The Crosstalk Between Tumor-Associated Macrophages (TAMs) and Tumor Cells and the Corresponding Targeted Therapy

Tumor microenvironment (TME) is composed of tumor cells and surrounding non-tumor stromal cells, mainly including tumor associated macrophages (TAMs), endothelial cells, and carcinoma-associated fibroblasts (CAFs). The TAMs are the major components of non-tumor stromal cells, and play an important role in promoting the occurrence and development of tumors. Macrophages originate from bone marrow hematopoietic stem cells and embryonic yolk sacs. There is close crosstalk between TAMs and tumor cells. With the occurrence of tumors, tumor cells secrete various chemokines to recruit monocytes to infiltrate tumor tissues and further promote their M2-type polarization. Importantly, M2-like TAMs can in turn accelerate tumor growth, promote tumor cell invasion and metastasis, and inhibit immune killing to promote tumor progression. Therefore, targeting TAMs in tumor tissues has become one of the principal strategies in current tumor immunotherapy. Current treatment strategies focus on reducing macrophage infiltration in tumor tissues and reprogramming TAMs to M1-like to kill tumors. Although these treatments have had some success, their effects are still limited. This paper mainly summarized the recruitment and polarization of macrophages by tumors, the support of TAMs for the growth of tumors, and the research progress of TAMs targeting tumors, to provide new treatment strategies for tumor immunotherapy.
Cortical Patterns of Pleasurable Musical Chills Revealed by High-Density EEG

Music has the capacity to elicit strong positive feelings in humans by activating the brain’s reward system. Because group emotional dynamics is a central concern of social neurosciences, the study of emotion in natural/ecological conditions is gaining interest. This study aimed to show that high-density EEG (HD-EEG) is able to reveal patterns of cerebral activities previously identified by fMRI or PET scans when the subject experiences pleasurable musical chills. We used HD-EEG to record participants (11 female, 7 male) while listening to their favorite pleasurable chill-inducing musical excerpts; they reported their subjective emotional state from low pleasure up to chills. HD-EEG results showed an increase of theta activity in the prefrontal cortex when arousal and emotional ratings increased, which are associated with orbitofrontal cortex activation localized using source localization algorithms. In addition, we identified two specific patterns of chills: a decreased theta activity in the right central region, which could reflect supplementary motor area activation during chills and may be related to rhythmic anticipation processing, and a decreased theta activity in the right temporal region, which may be related to musical appreciation and could reflect the right superior temporal gyrus activity. The alpha frontal/prefrontal asymmetry did not reflect the felt emotional pleasure, but the increased frontal beta to alpha ratio (measure of arousal) corresponded to increased emotional ratings. These results suggest that EEG may be a reliable method and a promising tool for the investigation of group musical pleasure through musical reward processing.
Why Is It Hard to Fight Herding?

The ubiquity of information, in part a consequence of the fast growth of Internet technologies, provides individuals with previously unknown opportunities to acquire and share information about new technology products. We witness numerous situations where potential adopters observe the decisions (but not the reasoning) of others and imitate their adoption behaviors. This implies that herd behavior can lead to en mass adoption. However, individuals possessing different characteristics exhibit different degrees of herd behavior. The characteristics of a given technology must also fit with the requirements of the task(s) that a technology adopter wants to fulfill. It is important to understand these phenomena in the herding context because they can influence a technology's staying power. We examine how several different user and technology characteristics interact with the antecedents of herd behavior, observed popularity of prior adoption and perceived uncertainty, to predict one's individual propensity for imitation in technology adoption. We test our research model via an online experiment with 260 respondents. One key finding is that while prior research has not found uncertainty to have the expected effect on propensity to imitate, it does in fact have a significant effect when various individual difference and technology moderators are taken into account.
Differentiation of Human induced Pluripotent Stem Cells to Authentic Macrophages using Fully Defined, Serum Free, Open Source Media

Summary Human iPSC and macrophages derived from them are increasingly popular tools for research into both infectious and degenerative diseases. However, as the field strives for greater modelling accuracy, it is becoming ever more challenging to justify the use of undefined and proprietary media for the culture of these cells. We describe here two fully defined, serum-free, open-source media for the culture of iPSC and differentiation of iPSC-derived macrophages. These media are equally capable of maintaining these cells compared to commercial alternatives. The macrophages differentiated in these defined media display improved terminally differentiated cell characteristics, reduced basal expression of induced anti-viral response genes, and improved polarisation capacity. We conclude that cells cultured in these media are an appropriate and malleable model for tissue resident macrophages, on which future differentiation techniques can be built.
A booster dose enhances immunogenicity of the COVID-19 vaccine candidate ChAdOx1 nCoV-19 in aged mice

The spread of SARS-CoV-2 has caused a global pandemic that has affected almost every aspect of human life. The development of an effective COVID-19 vaccine could limit the morbidity and mortality caused by infection, and may enable the relaxation of social distancing measures. Age is one of the most significant risk factors for poor health outcomes after SARS-CoV-2 infection, therefore it is desirable that any new vaccine candidates should elicit a robust immune response in older adults. Here, we test the immunogenicity of the adenoviral vectored vaccine ChAdOx1 nCoV-19 (AZD-1222) in aged mice. We find that a single dose of this vaccine induces cellular and humoral immunity in aged mice, but at a reduced magnitude than in younger adult mice. Furthermore, we report that a second dose enhances the immune response to this vaccine in aged mice, indicating that a primeboost strategy may be a rational approach to enhance immunogenicity in older persons.
Lipidomic Profiling of Clinical Prostate Cancer Reveals Targetable Alterations in Membrane Lipid Composition

This study identifies malignancy and treatment-associated changes in lipid composition of clinical prostate cancer tissues, suggesting that mediators of these lipidomic changes could be targeted using existing metabolic agents. Dysregulated lipid metabolism is a prominent feature of prostate cancer that is driven by androgen receptor (AR) signaling. Here we used quantitative mass spectrometry to define the “lipidome” in prostate tumors with matched benign tissues (n = 21), independent unmatched tissues (n = 47), and primary prostate explants cultured with the clinical AR antagonist enzalutamide (n = 43). Significant differences in lipid composition were detected and spatially visualized in tumors compared with matched benign samples. Notably, tumors featured higher proportions of monounsaturated lipids overall and elongated fatty acid chains in phosphatidylinositol and phosphatidylserine lipids. Significant associations between lipid profile and malignancy were validated in unmatched samples, and phospholipid composition was characteristically altered in patient tissues that responded to AR inhibition. Importantly, targeting tumor-related lipid features via inhibition of acetyl-CoA carboxylase 1 significantly reduced cellular proliferation and induced apoptosis in tissue explants. This characterization of the prostate cancer lipidome in clinical tissues reveals enhanced fatty acid synthesis, elongation, and desaturation as tumor-defining features, with potential for therapeutic targeting. Significance: This study identifies malignancy and treatment-associated changes in lipid composition of clinical prostate cancer tissues, suggesting that mediators of these lipidomic changes could be targeted using existing metabolic agents.
Epitope profiling reveals binding signatures of SARS-CoV-2 immune response and cross-reactivity with endemic HCoVs

A major goal of current SARS-CoV-2 vaccine efforts is to elicit antibody responses that confer protection. Mapping the epitope targets of the SARS-CoV-2 antibody response is critical for innovative vaccine design, diagnostics, and development of therapeutics. Here, we developed a phage display library to map antibody binding sites at high resolution within the complete viral proteomes of all human-infecting coronaviruses in patients with mild or moderate/severe COVID-19. The dominant immune responses to SARS-CoV-2 were targeted to regions spanning the Spike protein, Nucleocapsid, and ORF1ab. Some epitopes were identified in the majority of samples while others were rare, and we found variation in the number of epitopes targeted by different individuals. We also identified a set of cross-reactive sequences that were bound by antibodies in SARS-CoV-2 unexposed individuals. Finally, we uncovered a subset of enriched epitopes from commonly circulating human coronaviruses with significant homology to highly reactive SARS-CoV-2 sequences.
Distinct cellular immune profiles in the airways and blood of critically ill patients with COVID-19

Background Knowledge of the pathophysiology of COVID-19 is almost exclusively derived from studies that examined the immune response in blood. We here aimed to analyse the pulmonary immune response during severe COVID-19 and to compare this with blood responses. Methods This was an observational study in patients with COVID-19 admitted to the intensive care unit (ICU). Mononuclear cells were purified from bronchoalveolar lavage fluid (BALF) and blood, and analysed by spectral flow cytometry; inflammatory mediators were measured in BALF and plasma. Findings Paired blood and BALF samples were obtained from 17 patients, four of whom died in the ICU. Macrophages and T cells were the most abundant cells in BALF, with a high percentage of T cells expressing the ƴδ T cell receptor. In the lungs, both CD4 and CD8 T cells were predominantly effector memory cells (87·3% and 83·8%, respectively), and these cells expressed higher levels of the exhaustion marker programmad death-1 than in peripheral blood. Prolonged ICU stay (>14 days) was associated with a reduced proportion of activated T cells in peripheral blood and even more so in BALF. T cell activation in blood, but not in BALF, was higher in fatal COVID-19 cases. Increased levels of inflammatory mediators were more pronounced in BALF than in plasma. Interpretation The bronchoalveolar immune response in COVID-19 has a unique local profile that strongly differs from the immune profile in peripheral blood. Fully elucidating COVID-19 pathophysiology will require investigation of the pulmonary immune response.
Neuroimaging: into the Multiverse

For most neuroimaging questions the huge range of possible analytic choices leads to the possibility that conclusions from any single analytic approach may be misleading. Examples of possible choices include the motion regression approach used and smoothing and threshold factors applied during the processing pipeline. Although it is possible to perform a multiverse analysis that evaluates all possible analytic choices, this can be computationally challenging and repeated sequential analyses on the same data can compromise inferential and predictive power. Here, we establish how active learning on a low-dimensional space that captures the inter-relationships between analysis approaches can be used to efficiently approximate the whole multiverse of analyses. This approach balances the benefits of a multiverse analysis without the accompanying cost to statistical power, computational power and the integrity of inferences. We illustrate this approach with a functional MRI dataset of functional connectivity across adolescence, demonstrating how a multiverse of graph theoretic and simple pre-processing steps can be efficiently navigated using active learning. Our study shows how this approach can identify the subset of analysis techniques (i.e., pipelines) which are best able to predict participants’ ages, as well as allowing the performance of different approaches to be quantified.