Miracle-dz/UniFAR-FTUs huggingface dataset:
Portiera gives new clues on the evolutionary history of whiteflies

Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. Their taxonomy is currently based on the morphology of nymphal stages that display phenotypic plasticity, which produces inconsistencies. To overcome this limitation, we developed a new phylogenetic framework that targets five genes of Candidatus Portiera aleyrodidarum, the primary endosymbiont of whiteflies. Portiera lineages have been co-diverging with whiteflies since their origin and therefore reflect their host evolutionary history. We also studied the origin of stability and instability in Portiera genomes by testing for the presence of two alternative gene rearrangements and the loss of a functional polymerase proofreading subunit (dnaQ), previously associated with genome instability. We present two phylogenetic reconstructions. One using the sequences of all five target genes from 22 whitefly species belonging to 17 genera. The second uses only two genes to include additional published Portiera sequences of 21 whitefly species, increasing our sampling size to 42 species from 25 genera. The developed framework showed low signal saturation, specificity to whitefly samples, and efficiency in solving inter-genera relationships and standing inconsistencies in the current taxonomy of the superfamily. Genome instability was found to be present only in the Aleurolobini tribe containing the Singhiella, Aleurolobus and Bemisia genera. This suggests that Portiera genome instability likely arose in the Aleurolobini tribe’s common ancestor, around 70 Mya. We propose a link between the switch from multi-bacteriocyte to a single-bacteriocyte mode of inheritance in the Aleurolobini tribe and the appearance of genome instability in Portiera.
Conjugal DNA transfer in the maternally inherited symbiont of tsetse flies Sodalis glossinidius

Stable associations between insects and bacterial species are widespread in nature. This is the case for many economically important insects, such as tsetse flies. Tsetse flies are the vectors of Trypanosoma brucei, the etiological agent of African trypanosomiasis—a zoonotic disease that incurs a high socioeconomic cost in endemic regions. Populations of tsetse flies are often infected with the bacterium Sodalis glossinidius. Following infection, S. glossinidius establishes a chronic, stable association characterized by vertical (maternal) and horizontal (paternal) modes of transmission. Due to the stable nature of this association, S. glossinidius has been long sought as a means for the implementation of anti-Trypanosoma paratransgenesis in tsetse flies. However, the lack of tools for the genetic modification of S. glossinidius has hindered progress in this area. Here we establish that S. glossinidius is amenable to DNA uptake by conjugation. We show that conjugation can be used as a DNA delivery method to conduct forward and reverse genetic experiments in this bacterium. This study serves as an important step in the development of genetic tools for S. glossinidius. The methods highlighted here should guide the implementation of genetics for the study of the tsetse-Sodalis association and the evaluation of S. glossinidius-based tsetse fly paratransgenesis strategies. Importance Tsetse flies are the insect vectors of T. brucei, the causative agent of African sleeping sickness—a zoonotic disease that inflicts a substantial economic cost to a broad region of sub-Saharan Africa. Notably, tsetse flies can be infected with the bacterium S. glossinidius to establish an asymptomatic chronic infection. This infection can be inherited by future generations of tsetse flies allowing S. glossinidius to spread and persist within populations. To this effect, S. glossinidius has been considered as a potential expression platform to create flies which reduce T. brucei stasis and lower overall parasite transmission to humans and animals. However, the efficient genetic manipulation of S. glossinidius has remained a technical challenge due to its complex growth requirements and uncharacterized physiology. Here we exploit a natural mechanism of DNA transfer among bacteria and develop an efficient technique to genetically manipulate S. glossinidius for future studies in reducing trypanosome transmission.
Monogamy in a Moment: How do Brief Social Interactions Change Over Time in Pair-Bonded Zebra Finches (Taeniopygia guttata)?

Research on monogamy has largely focused on marked behaviors that are unique to pair bonded partners. However, these marked behaviors represent only a subset of the pair-directed behaviors that partners engage in; the influence of pair bonding on mundane or subtle social interactions among partners remains largely unknown. In the current study, we describe the changes that occur during brief social reunions (or greets) over the course of pair bonding in zebra finches. We quantified pair-directed behavior during five-minute reunions from three stages of pair bonding: initial pairing (between 4-72 hrs), early pairing (1-2 weeks) and late pairing (>1 month). These social interactions were operationalized in multiples ways. First, we quantified the overall activity levels (call and movement rates) for both the male and female. Overall, females were more active than males, but for both males and females calling activity was highest during the initial timepoint (between 4-72 hrs post-pairing). We quantified behavioral coordination between partners in two ways, 1) similarity in call and movement rates between partners, and 2) temporal synchrony between calls and movements (via sliding correlation coefficients of time-stamped calls and movements). Overall there were no effects of pairing on behavioral coordination. Finally, we used principal component analyses to disentangle behavioral coordination from the activity levels of the male and female. These results contribute to a growing line of evidence that male and female zebra finches differentially contribute to social dynamics and highlight the influence of pair bonding on the development of social dynamics. Behavioral coordination is clearly important for marked interactions (e.g. duetting, courtship displays and biparental care). Our results raise the question of what the roles of such mundane social interactions are in monogamous partnerships.
An Age-Specific Atlas for Delineation of White Matter Pathways in Children Aged 6-8 Years

Diffusion MRI allows non-invasive assessment of white matter maturation in typical development and of white matter damage due to brain injury or pathology. Reliably attributing diffusion metrics to specific white matter pathways either requires use of lengthy acquisition protocols with numerous diffusion directions, which may be problematic in certain cohorts (e.g. children or adults with mild cognitive impairment), or probabilistic white matter atlases, which allow delineation of white matter tracts without the need to perform tractography, thus eliminating the need for the extensive scans required for modern tractography algorithms. However, given the known age-dependency of developmental change in white matter it may not be optimal to use an adult template when assessing data acquired from children. This study develops an age-specific probabilistic white matter atlas for delineation of 12 major white matter tracts in children aged 6-8 years. By comparing to fibre tracking in individuals, we demonstrate that this age-specific atlas gives better overall performance than simply registering to the Johns Hopkins University (JHU) adult white matter template in both data acquired from a single cohort on a single scanner (age-specific r = 0.72; JHU r = 0.54) and from a cohort taken from the ABIDE dataset (age-specific r = 0.75; JHU r = 0.72). Accuracy was assessed by comparing estimates of tract-level diffusion metrics, using the age-specific and adult templates, to results of subject-specific tracing. To our knowledge, this is the first publicly available probabilistic atlas of white matter tracts for this age group. We then use the age-specific atlas to provide evidence for reduced fractional anisotropy in several tracts in children who were treated with therapeutic hypothermia for neonatal encephalopathy at birth and did not have cerebral palsy, compared with controls matched for age, sex and socio-economic status.
A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response

Cancer treatments can be highly toxic and frequently only a subset of the patient population will benefit from a given treatment. Tumour genetic makeup plays an important role in cancer drug sensitivity. We suspect that gene expression markers could be used as a decision aid for treatment selection or dosage tuning. Using in vitro cancer cell line dose-response and gene expression data from the Genomics of Drug Sensitivity in Cancer (GDSC) project, we build a dose-varying regression model. Unlike existing approaches, this allows us to estimate dosage-dependent associations with gene expression. We include the transcriptomic profiles as dose-invariant covariates into the regression model and assume that their effect varies smoothly over the dosage levels. A two-stage variable selection algorithm (variable screening followed by penalised regression) is used to identify genetic factors that are associated with drug response over the varying dosages. We evaluate the effectiveness of our method using simulation studies focusing on the choice of tuning parameters and cross-validation for predictive accuracy assessment. We further apply the model to data from five BRAF targeted compounds applied to different cancer cell lines under different dosage levels. We highlight the dosage-dependent dynamics of the associations between the selected genes and drug response, and we perform pathway enrichment analysis to show that the selected genes play an important role in pathways related to tumourgenesis and DNA damage response. Author Summary Tumour cell lines allow scientists to test anticancer drugs in a laboratory environment. Cells are exposed to the drug in increasing concentrations, and the drug response, or amount of surviving cells, is measured. Generally, drug response is summarized via a single number such as the concentration at which 50% of the cells have died (IC50). To avoid relying on such summary measures, we adopted a functional regression approach that takes the dose-response curves as inputs, and uses them to find biomarkers of drug response. One major advantage of our approach is that it describes how the effect of a biomarker on the drug response changes with the drug dosage. This is useful for determining optimal treatment dosages and predicting drug response curves for unseen drug-cell line combinations. Our method scales to large numbers of biomarkers by using regularisation and, in contrast with existing literature, selects the most informative genes by accounting for drug response at untested dosages. We demonstrate its value using data from the Genomics of Drug Sensitivity in Cancer project to identify genes whose expression is associated with drug response. We show that the selected genes recapitulate prior biological knowledge, and belong to known cancer pathways.
The hypothalamus as a hub for SARS-CoV-2 brain infection and pathogenesis

Most patients with COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), display neurological symptoms, and respiratory failure in certain cases could be of extra-pulmonary origin. Hypothalamic neural circuits play key roles in sex differences, diabetes, hypertension, obesity and aging, all risk factors for severe COVID-19, besides being connected to olfactory/gustative and brainstem cardiorespiratory centers. Here, human brain gene-expression analyses and immunohistochemistry reveal that the hypothalamus and associated regions express angiotensin-converting enzyme 2 and transmembrane proteinase, serine 2, which mediate SARS-CoV-2 cellular entry, in correlation with genes or pathways involved in physiological functions or viral pathogenesis. A post-mortem patient brain shows viral invasion and replication in both the olfactory bulb and the hypothalamus, while animal studies indicate that sex hormones and metabolic diseases influence this susceptibility.
RNA-seq Data and Alternative Splicing a General Understanding

RNA splicing is recognized as a very important exception of ”one gene – one protein” in genetics. There are intervening sequences called the introns (non-coding regions) laid between the exons (protein-coding regions). The number and length of introns (which seems useless for expression) increases greatly with evolutionary complexity. What makes the situation more complex, RNA splicing results a pre-mRNA or primary gene transcript translating into different protein isoforms, say multiple proteins come from only one gene (see [4], p.12). RNA splicing is a means to increase the diversity of proteins which is encoded by several genomes. In humans, roughly 95% of multiexonic genes, which are genes have more than one exon, are alternatively spliced (see [8]; Wiki, Alternative splicing). Nearly every biological process in mammals includes at least one gene that is alternatively spliced (see [4], p.14). RNA splicing removes introns from pre-mRNA transcripts by spliceosome (a complex RNA/protein machine) (see [1], p.262). It has been recognized that the mechanisms behind alternative splicing are extremely variable. Researchers’ goal is to predict the splicing, say, under particular conditions (as splicing codes), which alternative splicing products will produce (see Wiki, Alternative splicing). For example, Brendel and Kleffe applied trained logitlinear models in splice predictor, and Genie used neural network to splice sites (see [6], p.369). Splicing variants also may result in some diseases, like cancer (see Wiki, Alternative splicing). There are five basic modes of alternative splicing (see [4], p.13; Wiki, Alternative splicing). First, in the mode of exon skipping, which is the most common mode in pre-mRNAs, one exon could be spliced out of or retained. Second, in the mode of mutually exclusive exons, one and only one exon is retained. Third, in the mode of alternative donor site, alternative 5’ splice
Hierarchy-Aware Global Model for Hierarchical Text Classification

Hierarchical text classification is an essential yet challenging subtask of multi-label text classification with a taxonomic hierarchy. Existing methods have difficulties in modeling the hierarchical label structure in a global view. Furthermore, they cannot make full use of the mutual interactions between the text feature space and the label space. In this paper, we formulate the hierarchy as a directed graph and introduce hierarchy-aware structure encoders for modeling label dependencies. Based on the hierarchy encoder, we propose a novel end-to-end hierarchy-aware global model (HiAGM) with two variants. A multi-label attention variant (HiAGM-LA) learns hierarchy-aware label embeddings through the hierarchy encoder and conducts inductive fusion of label-aware text features. A text feature propagation model (HiAGM-TP) is proposed as the deductive variant that directly feeds text features into hierarchy encoders. Compared with previous works, both HiAGM-LA and HiAGM-TP achieve significant and consistent improvements on three benchmark datasets.
Plant response to irrigation with saline water in a Sicilian vineyard: results of a three-years field investigation

This paper reports the results of a three-year field investigation carried out in a vineyard located in Sicily (Mazara del Vallo, Trapani) within the framework of the Project: Evolution of cropping systems as affected by climate change (CLIMESCO). Research investigated soil-plant response to irrigation performed with water having two different salinity levels; soil hydrological characteristics, soil salinity, crop transpiration and stomatal conductance were measured in field plots. The results proved that crop transpiration and stomatal conductance were significantly affected by soil salinity conditions (expressed as electrical conductivity of the soil saturated water extract). A significant reduction in both the physiological parameters was observed in the treatment irrigated with water having higher salinity (electrical conductivity equal to 1.6 dS m-1) as compared to the treatment irrigated with water of lower salinity (electrical conductivity equal to 0.6 dS m-1).
All India Institute of Medical Sciences Triage Protocol (ATP): ATP of a Busy Emergency Department

Emergency department (ED), the specialty of undifferentiated resuscitation and care, caters all patients irrespective of their age, gender, social status, or disease condition. In doing so, the demand almost always outstrips the supply. To handle this demand-supply mismatch, ED triage is one of the measures. It is a carefully structured process in which patients are categorized to subsequent groups according to the severity of their presenting condition. [1]
Coexistence of ten-eleven translocation 2 and calreticulin mutations in myeloproliferative neoplasms: Possible prognostic value

Background: Mutations in the genes regulating epigenetic factors such as Ten-Eleven Translocation 2 (TET2) along with other mutations are highly effective in the patient's prognosis. The aim of this study was to evaluate the prevalence of TET2 and calreticulin (CALR) mutations among myeloproliferative neoplasms (MPNs) patients to determine if there is a prognostic value for these mutations coexistence. Materials and Methods: Blood sample was collected from patients. For the evaluation of mutations, polymerase chain reaction (PCR) was performed on the patient's DNA and PCR products were subsequently sequenced. Results: No significant correlation between coexistence of TET2 and CALR mutations with complete blood count parameters in patients was seen. However, platelet count was lower in patients with TET2 and CALR mutations compared with patients with CALR mutations only. Conclusion: The coexistence of CALR and TET2 mutations in MPN patients can be used as a prognostic factor.
Seasonal development of hypolimnetic ciliate communities in a eutrophic pond

The ciliated protozoan communities in the hypolimnion of a highly produtive pond were investigated over two years. Three physiological groups could be distinguished: stratified water column; (b) anaerobic ciliates with endosymbiotic methanogens; and (c) anaerobes without endosymbiotic methanogens. Both groups of anaerobes were confined to the anoxic zone of the hypolimnion. Community biomass was dominated by microaerobic ciliates which had on average 20 times larger cells than anaerobic ciliates. Abundance and biomass of microaerobic ciliates decreased over the summer, while anaerobic ciliates increased. This reflected a spatial shift in the availability of inorganic nutrients and, as a result, of ciliate food from the epi- and metalimnion to the hypolimnion. The low biomass production of anaerobic ciliates was consistent with the low theoretical growth efficiency of anaerobic metabolism. Ciliate species displayed characteristic spatial and seasonal distribution patterns within the water column which were similar in both years investigated. Spatial and temporal distribution was mainly governed by two factors: (1) the distribution of dissolved oxygen; and (2) the availability of food. Distribution patterns were not related to chemical gradients other than the oxygen gradient, but they were correlated with the distribution of major food sources.
ADL-dependency, D-Dimers, LDH and absence of anticoagulation are independently associated with one-month mortality in older inpatients with Covid-19

Background: To assess factors associated with one-month mortality among older inpatients with Covid-19. Results: The mean age was 78 ± 7.8 years, 55.5% were men, CT scan lung damage was observed in 76% of the patients (mild 23%, moderate 38%, extensive 22%, and severe 7%). The mortality rate was 26%. Dependency/Activities of Daily Living (ADL) score ≤ 5/6, D-Dimers, LDH, and no anticoagulation by reference for curative were independently associated with one-month mortality. A score derived from the multivariate model showed good calibration and very good discrimination (Harrell’s C index [95%CI] = 0.83 [0.79-0.87]). Conclusion: ADL-dependency, high serum levels of D-Dimers and LDH and the absence of anticoagulation were independently associated with one-month mortality among older inpatients with Covid-19. Methods: 108 consecutive older inpatients aged 65 and over with Covid-19 confirmed by RT-PCR and/or typical CT chest scan were prospectively included in a French single-centre cohort study from March to April 2020. A systematic geriatric assessment was performed. Covariates were lymphocyte count, serum levels of albumin, C-Reactive Protein, D-Dimers and Lactate Dehydrogenase (LDH), anticoagulation level, and exposure to the hydroxychloroquine and azithromycin combined therapy. Cox uni- and multivariate proportional-hazard regressions were performed to identify predictors of one-month mortality.
History of Paclitaxel and Oral Paclitaxel – Clinical Data and Future

The most known natural source cancer drug is paclitaxel, which is derived from the tough protective outer sheath of the trunk and branches (referred as bark) of the Pacific yew tree (Taxus brevifolia). [1] Paclitaxel has demonstrated a wide spectrum of antitumor activity as a single agent and also in combination with other chemotherapeutic agents as part of combination regimens. [2] It is used extensively in the treatment of advanced carcinomas of the breast, ovarian cancer, nonsmall cell lung cancer, and other solid tumors.
Is intraoperative supplementation of dextrose essential for infants undergoing facial cleft surgeries?

Background and Aims: Dextrose is commonly added to the intraoperative maintenance fluids of pediatric patients. The primary objective was to evaluate the effect of addition of 1% dextrose to Ringer's lactate (RL) on blood glucose levels in infants undergoing facial cleft surgeries. Material and Methods: This prospective, randomized, single blinded study was conducted in forty infants undergoing either cheiloplasty or palatoplasty. Random blood sugar (RBS) was assessed using a glucometer after induction of anaesthesia, and at 1 and 2 hours later. Group R received RL and Group D received RL with 1% dextrose as intraoperative maintenance fluid. Hypoglycemia was defined as RBS <70 mg/dL and hyperglycemia as RBS >150 mg/dL. Results: Baseline RBS levels and those at 60 min and 120 min post-induction were comparable in both groups. The increase in blood sugar levels from baseline to 60 min and to 120 min in each group was significant. Incidence of hyperglycemia was comparable in both groups. There were no episodes of hypoglycemia, intraoperatively. Conclusion: Use of Ringer lactate alone or with addition of 1% dextrose resulted in comparable intraoperative blood sugar levels when used as maintenance fluid in infants undergoing facial cleft surgeries.