Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of Pelagic and Benthic Bacterial Assemblages in the Western Pacific Ocean

Despite numerous studies on marine prokaryotes, the vertical distribution patterns of bacterial community, either on the taxonomic composition or the functional structure, remains relatively unexplored. Using HiSeq-derived 16S rRNA data, the depth-related distribution patterns of taxonomic diversity and functional structure predicted from diversity data in the water column and sediments of the Western Pacific Ocean were explored. The OTU richness declined along the water column after peaking between 100 to 200 m deep. Relative abundance of Cyanobacteria and SAR11 decreased significantly with depth, while Actinobacteria and Gammaproteobacteria increased. This clearly mirrors the vertical distribution pattern of the predicted functional composition with the shift between phototrophic to chemoheterotrophic groups from the surface to the deeper layers. In terms of community composition and functional structure, the epipelagic zone differed from other deeper ones (i.e., meso-, bathy-, and abyssopelagic zones) where no obvious differences were detected. For the epipelagic zone, temperature, dissolved oxygen, and salinity were recognized as the crucial factors shaping both community composition and the functional structure of bacteria. Compared with water samples, benthic sediment samples harbored unexpectedly higher read abundance of Proteobacteria, presenting distinguishable taxonomic and functional compositions. This study provides novel knowledge on the vertical distribution of bacterial taxonomic and functional compositions in the western Pacific.
Acute Hypoxemic Respiratory Failure in Immunocompromised Patients: Taking Aggressive Measures to Identify Etiology

Immunocompromised patients often experience pulmonary complications especially acute respiratory failure (ARF) (1–3), themain cause of which is infection (4). To avoid increasing the risk of infection, non-invasive mechanical ventilation (NIV) is recommended as a first line treatment for immunocompromised patients (5, 6). However, recent studies have cast some doubts on the protective effects of NIV as a first-line treatment in immunocompromised patients with ARF (7– 9). Meanwhile, a high-flow nasal cannula (HFNC) may potentially be a better alternative to NIV or standard oxygenation therapy (SOT) in immunocompromised patients due to its unique functions (4), but the results of studies of the effect of HFNC are also obscure (10–12). It has been determined that the identification of ARF etiology in immunocompromised patients currently contributes extensively to the survival rates of these patients. Recently, Azoulay et al. (13) conducted a large, multinational prospective cohort study named the Efraim study, in which 1,611 critically ill immunocompromised patients with ARF were enrolled. They compared the intubation rate between four groups: standard oxygen only, HFNC only, NIV only, and both HFNC+NIV. Meanwhile, they also included patients who received firstline invasive mechanical ventilation (IMV) and all-cause hospital mortality rates were compared between these groups. The study illustrated that the use of NIV did not impact outcomes. Although HFNC reduced the intubation rate, it did not influence all-cause hospital mortality. However, more importantly, they found that the etiology of ARF had an impact on hospital mortality, acting as a vital confounder in the association between oxygenation strategy and mortality, and the study proved that patients with undetermined ARF have a very high mortality rate.
Age-Dependent Assessment of Genes Involved in Cellular Senescence, Telomere, and Mitochondrial Pathways in Human Lung Tissue of Smokers, COPD, and IPF: Associations With SARS-CoV-2 COVID-19 ACE2-TMPRSS2-Furin-DPP4 Axis

Background Aging is one of the key contributing factors for chronic obstructive pulmonary diseases (COPD) and other chronic inflammatory lung diseases. Here, we determined how aging contributes to the altered gene expression related to mitochondrial function, cellular senescence, and telomeric length processes that play an important role in the progression of COPD and idiopathic pulmonary fibrosis (IPF). Methods Total RNA from the human lung tissues of non-smokers, smokers, and patients with COPD and IPF were processed and analyzed using a Nanostring platform based on their ages (younger: <55 years and older: >55 years). Results Several genes were differentially expressed in younger and older smokers, and patients with COPD and IPF compared to non-smokers which were part of the mitochondrial biogenesis/function (HSPD1, FEN1, COX18, COX10, UCP2 & 3), cellular senescence (PCNA, PTEN, KLOTHO, CDKN1C, TNKS2, NFATC1 & 2, GADD45A), and telomere replication/maintenance (PARP1, SIRT6, NBN, TERT, RAD17, SLX4, HAT1) target genes. Interestingly, NOX4 and TNKS2 were increased in the young IPF as compared to the young COPD patients. Genes in the mitochondrial dynamics and quality control mechanisms like FIS1 and RHOT2 were decreased in young IPF compared to their age matched COPD subjects. ERCC1 and GADD45B were higher in young COPD as compared to IPF. Aging plays an important role in various infectious diseases including the SARS-CoV-2 infection. Lung immunoblot analysis of smokers, COPD and IPF subjects revealed increased abundance of proteases and receptor/spike protein like TMPRSS2, furin, and DPP4 in association with a slight increase in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor ACE2 levels. Conclusions Overall, these findings suggest that altered transcription of target genes that regulate mitochondrial function, cellular senescence, and telomere attrition in the pathobiology of lung aging in COPD and IPF is associated with alterations in SARS-CoV-2 ACE2-TMPRSS2-Furin-DPP4 axis as pharmacological targets for COVID-19.
High Occurrence of Bacterial Competition Among Clinically Documented Opportunistic Pathogens Including Achromobacter xylosoxidans in Cystic Fibrosis

Cystic Fibrosis (CF) airways favor abnormal microbial development. Infections are considered as polymicrobial and competition can be observed between microorganisms. The current literature on bacterial competition in CF mostly consists of studies with limited numbers of strains, mainly focused on the major pathogens Pseudomonas aeruginosa (Pa) and Staphylococcus aureus (Sa) and does not give a comprehensive overview of the overall importance of bacterial interactions or the behavior of less often encountered emerging bacteria such as Achromobacter. In this context, we screened a panel of 39 strains from six CF patients, of either clinical or domestic environmental origin, distinguished according to genotype and belonging to four opportunistic pathogens, Pa (n = 15), Sa (n = 3), Stenotrophomonas maltophilia (Sm, n = 10) and Achromobacter xylosoxidans (Ax, n = 11). We investigated their capacity to compete in terms of growth, motility, and pigment production on agar media through 203 crossing experiments. Eleven strains selected via the initial screening results were further studied for competitive growth in liquid medium and biofilm formation. Competition was noted for 33% (67/203) of the pairs of strains with 85 modifications observed between monocultures and co-cultures, impacting growth (23.6%), motility (13.8%), and/or pigment production (6.1%). Under all conditions of the study (clinical, environmental strains; intra-, inter-patients; intra-, inter-species levels), competition was significantly more frequent among pairs of strains with at least one clinical strain. While Pa mainly outcompeted other species, in one patient with chronic colonization by Ax and sporadic colonization by Pa, we showed that some Ax inhibited the growth and pigmentation of Pa whereas biofilm formation was drastically reduced. Enlarging the panel of strains tested in competition assays gave new perspectives on the complex interactions taking place among the CF airway community. Indeed, the frequent occurrence of varied, strain-dependent interactions is revealed here. We report the first results of competition assays for Ax with the ability of certain strains to outcompete Pa. Our results are linked to the patient’s colonization history and question the importance of bacterial competitiveness in the colonization pattern of CF airways.
Shape Correspondence by Aligning Scale-invariant LBO Eigenfunctions

When matching non-rigid shapes, the regular or scale-invariant Laplace-Beltrami Operator (LBO) eigenfunctions could potentially serve as intrinsic descriptors which are invariant to isometric transformations. However, the computed eigenfunctions of two quasi-isometric surfaces could be substantially different. Such discrepancies include sign ambiguities and possible rotations and reﬂections within subspaces spanned by eigenfunctions that correspond to similar eigenvalues. Thus, without aligning the corresponding eigenspaces it is difﬁcult to use the eigenfunctions as descriptors. Here, we propose to model the relative transformation between the eigenspaces of two quasi-isometric shapes using a band orthogonal matrix, as well as present a framework that aims to estimate this matrix. Estimating this transformation allows us to align the eigenfunctions of one shape with those of the other, that could then be used as intrinsic, consistent, and robust descriptors. To estimate the transformation we use an unsupervised spectral-net framework that uses descriptors given by the eigenfunctions of the scale-invariant version of the LBO. Then, using a spectral training mechanism, we ﬁnd a band limited orthogonal matrix that aligns the two sets of eigenfunctions.
Modeling the potassium requirements of potato crop for yield and quality optimization

The intensity, quantity as well as capacity factors are important to predict the amount of nutrient in soil required for maximum plant growth. Sorption isotherm considers these three factors so believed to be one of the most important techniques in soil which control the fate and mobility of nutrients. The field experiment was conducted to find out site-specific and crop-specific potassium requirement for potato crop. The potassium adsorption isotherm was constructed and Freundlich model was used to theoretically work out different soil solution K levels (0, 5, 10, 15, 20, 25, and 30 mg L). The K fertilizer doses were calculated against these specific soil solution levels. Field experiment was conducted with seven model based K fertilizer treatments (0, 49, 94, 139, 183, 228, and 273 kg K ha) and three replications in Randomized Complete Block Design (RCBD) using potato as test crop. The results showed that growth parameters like plant height, leaf area and chlorophyll significantly contributed to potato tuber yield. Different yield response models were tested and it was observed that linear plus plateau and quadratic plus plateau predicted equally well the optimum fertilizer K rate both for yield and quality attributes of potato. For maximum potato tuber yield i.e.34.41 Mg ha the economic optimum K was 100 kg ha. Optimum fertilizer K rates (at 95 % relative yield) for potato tuber yield, dry matter percentage, protein, starch contents and vitamin C contents were 100, 103, 180, 230 and 200 kg K ha, respectively. So, it is suggested that adsorption isotherm technique should be used to calculate site specific and crop specific fertilizer requirements of crops and 100 kg ha is recommended as optimum potassium fertilizer for potato crop. Moreover, the K fertilizer application would improve crop quality that would support the quality based marketing system in Pakistan.
Sickle Cell Anemia: Variants in the CYP2D6, CAT, and SLC14A1 Genes Are Associated With Improved Hydroxyurea Response

Differences in hydroxyurea response in sickle cell anemia may arise due to a series of factors with genetic factors appearing to be predominant. This study aims to investigate the effects of single nucleotide polymorphisms in genes encoding drug-metabolizing enzymes and solute carriers on hydroxyurea response, in patients with sickle cell anemia. For that purpose, a total number of 90 patients with sickle cell anemia were recruited, 45 were undergoing hydroxyurea treatment, while 45 were not under the treatment. Association analyses were performed between CYP3A4 (rs2740574), CYP2D6 (rs3892097), CAT (rs7943316 and rs1001179), and SLC14A1 (rs2298720) variants and laboratory parameters. According to our findings, patients with hydroxyurea treatment demonstrated higher HbF levels and a significant improvement in hemolytic, hepatic, inflammatory, and lipid parameters in comparison to those without the treatment. We also found significant associations between the CYP2D6 (rs3892097), CAT (rs7943316 and rs1001179), and SLC14A1 (rs2298720) variants and an improvement of the therapeutic effects, specifically the hemolytic, hepatic, inflammatory, lipid, and renal parameters. In conclusion, our results highlight the importance of the investigated variants, and their strong association with hydroxyurea efficacy in patients with sickle cell anemia, which may be considered in the future as genetic markers.
Tracking Changes in Frontal Lobe Hemodynamic Response in Individual Adults With Developmental Language Disorder Following HD tDCS Enhanced Phonological Working Memory Training: An fNIRS Feasibility Study

Background: Current research suggests a neurobiological marker of developmental language disorder (DLD) in adolescents and young adults may be an atypical neural profile coupled with behavioral performance that overlaps with that of normal controls. Although many imaging techniques are not suitable for the study of speech and language processing in DLD populations, fNIRS may be a viable option. In this study we asked if fNIRS can be used to identify atypical cortical activation patterns in individual adults with DLD and track potential changes in cortical activation patterns following a phonological working memory training protocol enhanced with anodal HD tDCS stimulation to the presupplementary motor area (preSMA). Objective/Hypothesis: The purpose of this study was two-fold: (1) to determine if fNIRS can be used to identify atypical hemodynamic responses in individual young adults with DLD during active spoken word processing and, (2) to determine if fNIRS can detect changes in hemodynamic response in these same adults with DLD following anodal HD tDCS enhanced phonological working memory training. Methods: Two adult subjects with DLD (female, age 25) completed a total of two sessions of fNIRs working memory task prior to and following one session of a non-word repetition task paired with anodal HD tDCS (1.0 mA tDCS; 20 min) to the preSMA. Standardized z-scores of behavioral measures (accuracy and reaction time) and changes in hemodynamic response during an n-back working memory task for the two participants with DLD was compared to that of a normative sample of 21 age- and gender- matched normal controls (ages 18 to 25) prior to and following phonological working memory training. Results: Individual standardized z-scores for each participant with DLD indicated that prior to training, hemoglobin response in the prefrontal lobe for both participants was markedly different from each other and normal controls. Following training, standard scores showed that the hemodynamic response for both participants moved within normal limits for ROIs. Conclusion: These findings highlight the feasibility of fNIRS to establish individual differences in the link between behavior and neural patterns in single subjects with DLD, as well as track individual differences in changes in brain activity following working memory training.
Biometrical Study of the Genitalia of Kano Brown Goats and Yankasa Sheep

Aim: To determine biometry of the female genitalia of Kano Brown goats and Yankasa sheep. Materials and Methods: Ninety-three samples (66 caprine and 27 ovine samples) of the entire reproductive tracts were collected and evaluated for biometrical dimensions. Results: There was no significant difference in ovarian biometry of the sheep and goat, except the differences in their widths and weights. Biometry of the vagina and cervix agrees with established documentation. Pregnancy did not affect length of the uterine body but increased length of the uterine horns. Non-pregnant uterine horn of the ewe was greater than doe’s in length and weight. Conclusion: It is inferred that biometrical status of female genital tract is essential in artificial insemination, and pregnancy diagnosis.
Relationship between intensity of blowfly infestation and reproductive success in a Corsican population of Blue Tits

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The Fragile X Mental Retardation Protein Regulates Striatal Medium Spiny Neuron Synapse Density and Dendritic Spine Morphology

The fragile X mental retardation protein (FMRP), an RNA-binding protein that mediates the transport, stability, and translation of hundreds of brain RNAs, is critically involved in regulating synaptic function. Loss of FMRP, as in fragile X syndrome (FXS), is a leading monogenic cause of autism and results in altered structural and functional synaptic plasticity, widely described in the hippocampus and cortex. Though FXS is associated with hyperactivity, impaired social interaction, and the development of repetitive or stereotyped behaviors, all of which are influenced by striatal activity, few studies have investigated the function of FMRP here. Utilizing a cortical-striatal co-culture model, we find that striatal medium spiny neurons (MSNs) lacking FMRP fail to make normal increases in PSD95 expression over a short time period and have significant deficits in dendritic spine density and colocalized synaptic puncta at the later measured time point compared to wildtype (WT) MSNs. Acute expression of wtFMRP plasmid in Fmr1 KO co-cultures results in contrasting outcomes for these measures on MSNs at the more mature time point, reducing spine density across multiple spine types but making no significant changes in colocalized puncta. FMRP’s KH2 and RGG RNA-binding domains are required for normal elimination of PSD95, and interruption of these domains slightly favors elimination of immature spine types. Further, KH2 is required for normal levels of colocalized puncta. Our data are largely consistent with a basal role for FMRP and its RNA-binding domains in striatal synapse stabilization on developing MSNs, and in light of previous findings, suggest distinct regional and/or cell type-specific roles for FMRP in regulating synapse structure.
Tumor-Infiltrating Lymphocytes and Their Prognostic Value in Cutaneous Melanoma

Recent breakthroughs in tumor immunotherapy such as immune checkpoint blockade (ICB) antibodies, have demonstrated the capacity of the immune system to fight cancer in a number of malignancies such as melanoma and lung cancer. The numbers, localization and phenotypes of tumor-infiltrating lymphocytes (TIL) are not only predictive of response to immunotherapy but also key modulators of disease progression. In this review, we focus on TIL profiling in cutaneous melanoma using histopathological approaches and highlight the observed prognostic value of the primary TIL subsets. The quantification of TIL in formalin-fixed tumor samples ranges from visual scoring of lymphocytic infiltrates in H&E to multiplex immunohistochemistry and immunofluorescence followed by enumeration using image analysis software. Nevertheless, TIL enumeration in the current literature primarily relies upon single marker immunohistochemistry analyses of major lymphocyte subsets such as conventional T cells (CD3, CD4, CD8), regulatory T cells (FOXP3) and B cells (CD20). We review key studies in the literature on associations between TIL subsets and patient survival. We also cover recent findings with respect to the existence of ectopic lymphoid aggregates found in the TME which are termed tertiary lymphoid structures (TLS) and are generally a positive prognostic feature. In addition to their prognostic significance, the existence of various TIL sub-populations has also been reported to predict a patient’s response to ICB. Thus, the literature on the predictive potential of TIL subsets in melanoma patients receiving ICB has also been discussed. Finally, we describe recently developed state-of-the-art profiling approaches for tumor infiltrating immune cells such as digital pathology scoring algorithms (e.g., Immunoscore) and multiplex proteomics-based immunophenotyping platforms (e.g., imaging mass cytometry). Translating these novel technologies have the potential to revolutionize tumor immunopathology leading to altering our current understanding of cancer immunology and dramatically improving outcomes for patients.
Salmonid Alphavirus Subtype 3 Induces Prolonged Local B Cell Responses in Atlantic Salmon (Salmo salar) After Intraperitoneal Infection

B cell responses are a crucial part of the adaptive immune response to viral infection. Infection by salmonid alphavirus subtype 3 (SAV3) causes pancreas disease (PD) in Atlantic salmon (Salmo salar) and is a serious concern to the aquaculture industry. In this study, we have used intraperitoneal (IP) infection with SAV3 as a model to characterize local B cell responses in the peritoneal cavity (PerC) and systemic immune tissues (head kidney/spleen). Intraperitoneal administration of vaccines is common in Atlantic salmon and understanding more about the local PerC B cell response is fundamental. Intraperitoneal SAV3 infection clearly induced PerC B cell responses as assessed by increased frequency of IgM+ B cells and total IgM secreting cells (ASC). These PerC responses were prolonged up to nine weeks post-infection and positively correlated to the anti-SAV3 E2 and to neutralizing antibody responses in serum. For the systemic immune sites, virus-induced changes in B cell responses were more modest or decreased compared to controls in the same period. Collectively, data reported herein indicated that PerC could serve as a peripheral immunological site by providing a niche for prolonged maintenance of the ASC response in Atlantic salmon.