Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlated activity favors synergistic processing in local cortical networks in vitro at synaptically relevant timescales

Abstract Neural information processing is widely understood to depend on correlations in neuronal activity. However, whether correlation is favorable or not is contentious. Here, we sought to determine how correlated activity and information processing are related in cortical circuits. Using recordings of hundreds of spiking neurons in organotypic cultures of mouse neocortex, we asked whether mutual information between neurons that feed into a common third neuron increased synergistic information processing by the receiving neuron. We found that mutual information and synergistic processing were positively related at synaptic timescales (0.05–14 ms), where mutual information values were low. This effect was mediated by the increase in information transmission—of which synergistic processing is a component—that resulted as mutual information grew. However, at extrasynaptic windows (up to 3,000 ms), where mutual information values were high, the relationship between mutual information and synergistic processing became negative. In this regime, greater mutual information resulted in a disproportionate increase in redundancy relative to information transmission. These results indicate that the emergence of synergistic processing from correlated activity differs according to timescale and correlation regime. In a low-correlation regime, synergistic processing increases with greater correlation, and in a high-correlation regime, synergistic processing decreases with greater correlation.
Mediterranean karst springs: diatom biodiversity hotspots under the pressure of hydrological fluctuation and nutrient enrichment

Abstract Mediterranean karst springs are affected by strong climatic seasonality, with long, dry and hot summers and are increasingly threatened by anthropogenic pressures. In Sardinia (western Mediterranean Sea, Italy), they are largely unexplored and their biocoenoses are mostly unknown. The diatom flora from two substrates (cobbles and macrophytes) in eight springs of different areas of the island was investigated in summer 2016 and winter 2017. A total of 162 diatom taxa (58 genera) were found of which 27 (17 genera) only on cobbles and 26 (18 genera) only on macrophytes. The most abundant species from both substrates were Achnanthidium minutissimum, Amphora indistincta, Amphora pediculus, Cocconeis euglypta, Planothidium frequentissimum and P. lanceolatum. Overall, 67 taxa (40 genera) were recorded in single sites and some of these taxa showed high affinity with specific environmental conditions. Hydrological stability (water flow permanence), discharge and nutrients were the main environmental factors influencing diatom assemblages. Our results suggest that diatoms can reflect important local factors related to the vulnerability of these spring ecosystems and underline the importance of their preservation both for biodiversity and water quality maintenance.
The realised velocity of climate change reveals remarkable idiosyncrasy of species’ distributional shifts

To date, our understanding of how species have shifted in response to recent climate warming has been based on a few studies with a limited number of species. Here we present a comprehensive, global overview of species’ distributional responses to changing climate across a broad variety of taxa (animals, plants, and fungi). We characterise species’ responses using a metric that describes the realised velocity of climate change: how closely species’ responses have tracked changing climate through time. In contrast to existing ‘climate velocity’ metrics that have focused on space, we focus on species and index their responses to a null expectation of change in order to examine drivers of inter-specific variation. Here we show that species are tracking climate on average, but not sufficiently to keep up with the pace of climate change. Further, species responses are highly idiosyncratic, and thus highlight that projections assuming uniform responses may be misleading. This is in stark contrast to species’ present-day and historical climate niches, which show strong evidence of the imprint of evolutionary history and functional traits. Our analyses are a first step in exploring the vast wealth of empirical data on species’ historic responses to recent climate change.
Assessment of Pruning and Controlled-release Fertilizer to Rejuvenate Huanglongbing-affected Sweet Orange

Previous research has shown that have a reduced root-to-shoot ratio, potentially due to the high rate of root death. The diminished root system cannot support the existing aboveground canopy and a cycle of imbalance begins. As a result, the tree enters into a continuous carbohydrate stress cycle and, eventually, the tree declines. Therefore, the goal of this study was to evaluate pruning as a strategy to adjust the root-to-shoot ratio to improve growth and pro- ductivity of HLB-affected trees. In Jan. 2015, a 3-year trial was initiated on a 14-year-old grove of ‘Hamlin’ sweet orange on Swingle citrumelo ( Citrus paradisi · Poncirus trifoliate ) rootstock that was symptomatic of HLB and produced less than 180 lb of fruit per tree. The four pruning treatments were as follows:
Comparative Evaluation of MIRONAUT-AM and CLSI broth microdilution method for antifungal susceptibility testing of Aspergillus species against four commonly used antifungals.

The aim of this study was to evaluate a colorimetric method, MIRONAUT-AM, for determining susceptibility testing of anidulafungin, amphotericin, voriconazole, and itraconazole by comparing the minimum inhibitory (effective) concentrations (MICs/MECs) obtained by this method to those generated by the reference Clinical Laboratory Standard Institute (CLSI) broth microdilution method. In sum, 78 clinical isolates of Aspergillus species, nine of them non-wild type (non-WT) with itraconazole MIC ranging from 2 mg/l to >16 mg/l, were tested against above antifungals. A. fumigatus ATCC 204305 was used as a reference strain, and test was performed in accordance with slightly modified yeast susceptibility testing instruction of the manufacture; conidia suspension inoculum and alamarBlue concentration were optimized. These same isolates were referred to Bristol Mycology reference laboratory and tested by CLSI method. The MICs and MECs generated by the two methods were compared using concordance analysis. MIRONAUT-AM showed significant concordance (P < .0001) with CLSI method, and overall agreement was high (≥90%). In addition, MIRONAUT-AM produced echinocandin MECs results within 18-24 hours incubation time and correctly detected all non-WT isolates except one isolate. This colorimetric method is very promising and appears to be a suitable alternative susceptibility testing method to labor intensive broth microdilution reference method for Aspergillus species.
Clozapine-induced nocturnal enuresis: diagnostic and treatment issues

Aims and Method To report the management of three cases of clozapine-induced enuresis, by description of these cases and literature review. Results Heavy sedation, generalised epilepsy and diabetes mellitus induced by clozapine are some of the mechanisms that underlie the emergence of this side-effect. Clinical Implications These cases illustrate several different pathophysiological mechanisms necessitating further diagnostic investigations before adequate treatment can be started. Clozapine-induced enuresis is probably under-reported owing to the embarrassing nature of this side-effect.
Pure line selection in a heterogeneous soybean cultivar

Although cultivars of autogamous plants are homogeneous genotypes, they may show natural variability due to mechanical mixing, natural hybridization, and mutation. The aim of the present study was to estimate genetic and phenotypic parameters and to identify and select superior genotypes that associate good performance in traits of interest from a heterogeneous population derived from the cultivar BRS Favorita RR. The evaluation experiments were carried out in two crop years and five cities of the state of Minas Gerais, Brazil, in a lattice design, using progenies and the control ‘BRS Favorita RR’. Plant height, first pod height, days to full maturity, lodging score, and grain yield were evaluated. For estimation of the variance components, analysis of deviance was performed by the restricted maximum likelihood (REML) method. The results show that there is difference among treatments and that it is possible to select progenies that outperform the control for all traits evaluated.
Fitness differences, not niche differences, limit species richness

A key question in ecology is what limits species richness. Coexistence theory presents the persistence of species amidst heterospecifics as a balance between niche differences and fitness differences that favour and hamper coexistence, respectively. With most applications focusing on species pairs, we know little about how niche and fitness differences respond to species richness, i.e. what constraints richness most. We present analytical proof that, in absence of higher-order interactions, the average fitness difference increases with richness, while the average niche difference stays constant. Analysis of a simple model with higher-order interactions, extensive simulations that relaxed all assumptions, and analyses of empirical data, confirmed these results. Our work thus shows that fitness differences, not niche difference, limit species richness. Our results contribute to the expansion of coexistence theory towards multi-species communities.
Can the devices used to treat obstructive sleep apnoea syndrome increase the tendency to gain weight

Amac: Bu calisma ile tikayici uyku apnesi sendromu (TUAS) hastalarinin tedavisinde kullanilan cihazlarin kilo degisiklikleri uzerine etkilerinin arastirilmasi planlandi. Yontem: Calismaya horlama ve uyku apnesi sikayetleriyle basvurup polisomnografi (PSG) tetkiki istenen 256 hasta dahil edildi. Hastalar apne hipopne indeksleri (AHI) ve cihaz kullanim durumlarina gore asagidaki sekilde gruplandirildi: Grup 1 TUAS tanisi konularak tedavi amacli cihaz kullananlar (n=101), Grup 2 TUAS tanisi konularak tedavi amacli onerilen cihaza uyum saglayamayanlar (n=76) ve Grup 3 PSG ile basit horlama teshisi konulup TUAS olmayanlar (n=79). Grup 1; CPAP, Auto CPAP veya BiPap kullanan hastalardan olusmaktadir. Her uc grup hastanin da vucut kitle indeksi (VKI) ve boyun cevresi (BC) olcumleri kayitlarina PSG merkezinden ulasildi (baslangic degerleri); bu hastalar tekrar olcum ve kontrol icin Kulak Burun Bogaz poliklinigine cagirilarak degerlendirildiler (kontrol degerleri). Bulgular: Grup 1 hastalarinda; baslangic degerleri ile kontrol degerleri karsilastirildiginda: VKI ve BC istatistiksel olarak anlamli derecede yuksekti (p 0.05). Grup 1 de farkli cihaz turlerini kullanan (CPAP, Auto CPAP veya BiPap) hastalar icin VKI ve BC acisindan anlamli farklilik gostermedi (p>0.05). Sonuc: Uyku apnesi hastalarini tedavi etmek icin kullanilan cihazlar kilo almaya egilimi arttirmaktadirlar. Bu hastalarin ileride kisir donguye sebep olmamak icin obezite acisindan yakin takipleri ve gerekli onlemlerin alinmasi gerekir. Anahtar sozcukler: Uyku apnesi, CPAP, Auto CPAP, BiPap, vucut kitle indeksi, boyun cevresi.
Dendrites with specialized glial attachments develop by retrograde extension using SAX-7 and GRDN-1

ABSTRACT Dendrites develop elaborate morphologies in concert with surrounding glia, but the molecules that coordinate dendrite and glial morphogenesis are mostly unknown. C. elegans offers a powerful model for identifying such factors. Previous work in this system examined dendrites and glia that develop within epithelia, similar to mammalian sense organs. Here, we focus on the neurons BAG and URX, which are not part of an epithelium but instead form membranous attachments to a single glial cell at the nose, reminiscent of dendrite-glia contacts in the mammalian brain. We show that these dendrites develop by retrograde extension, in which the nascent dendrite endings anchor to the presumptive nose and then extend by stretching during embryo elongation. Using forward genetic screens, we find that dendrite development requires the adhesion protein SAX-7/L1CAM and the cytoplasmic protein GRDN-1/CCDC88C to anchor dendrite endings at the nose. SAX-7 acts in neurons and glia, while GRDN-1 acts in glia to non-autonomously promote dendrite extension. Thus, this work shows how glial factors can help to shape dendrites, and identifies a novel molecular mechanism for dendrite growth by retrograde extension. Summary: Sensory dendrites attach at the nose of a C. elegans embryo and stretch out during embryo elongation. Their tips are anchored by SAX-7/L1CAM acting in neurons and glia, and by GRDN-1/CCDC88C acting in glia.
Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data

Motivation We participated in the DREAM Single Cell Transcriptomics Challenge. The challenge’s focus was two-fold; a) to identify the top 60, 40 and 20 genes that contain the most spatial information, and b) to reconstruct the 3-D arrangement of the D. melanogaster embryo using information from those genes. Results We developed two independent approaches, leveraging machine learning models from Lasso and Deep Neural Networks, that we successfully apply to high-dimensional single-cell sequencing data. Our methods allowed us to achieve top performance when compared to the ground truth. Among ~40 participating teams, the resulting solutions placed 10th, 6th, and 4th in the three DREAM sub-challenges #1, #2 and #3, respectively. Notably, for the Lasso approach we introduced a feature selection technique, Lasso-TopX, that allows a user to define a specific number of features they are interested in and the Neural Network approach utilizes weak supervision for linear regression to accommodate for uncertain or probabilistic training labels. Furthermore, we identified novel D. melanogaster genes that carry important positional information and were not previously suspected. Lastly, we show how the indirect use of the full datasets’ information can lead to data leakage and generate bias in overestimating the model’s performance. Availability https://github.com/TJU-CMC-Org/SingleCell-DREAM/. Contact Nestoras.Karathanasis@jefferson.edu
Perceptions of Patients Regarding Quality Nursing Care (QNC) at a Tertiary Care Hospital, Karachi, Pakistan

Background: Patients’ experiences regarding the quality of care continue to be a hot topic of discussion in the healthcare industry. Exploring the quality of nursing care from the patients’ perspectives is a vital element of quality evaluation. The purpose of this study was to explore the patients’ perspectives regarding quality nursing care.Methodology: A qualitative descriptive exploratory design was used. A total of twelve participants were recruited from one medical and one surgical unit at a tertiary care hospital in Karachi, Pakistan. Purposive sampling was used to select the participants. Data was collected through semi-structured interviews. A thematic analysis approach was used for data analysis.Results: Data analysis generated three main themes: (1) meaning of QNC, (2) characteristics of nurses, and (3) participants’ recommendations.Conclusion: Nursing care continues to be the foundation of healthcare and QNC could have a great effect on patients’ positive outcome of recovery and well- being. The study also provided vital implications for nursing administrators, practicing nurses, nursing, education, and research.
Enhanced insular connectivity with speech sensorimotor regions in trained singers – a resting-state fMRI study

The insula contributes to the detection and integration of salient events during goaldirected behavior and facilitates the interaction between motor, multisensory, and cognitive networks. Task-fMRI studies have suggested that experience with singing can enhance access to these resources. However, the long-term effects of vocal motor training on insula-based networks are currently unknown. In this study, we used restingstate fMRI to explore experience-dependent differences in insula co-activation patterns between conservatory-trained singers and non-singers. We found enhanced insula connectivity in singers compared to non-singers with constituents of the speech sensorimotor network, including the cerebellum (lobule VI, crus 2), primary somatosensory cortex, the parietal lobes, and the thalamus. Moreover, accumulated singing training correlated positively with increased co-activation in bilateral primary sensorimotor cortices in the somatotopic representations of the larynx (left dorsal anterior insula, dAI) and the diaphragm (bilateral dAI)—crucial regions for motorcortical control of complex vocalizations—together with the thalamus (bilateral posterior insula/left dAI) and the left putamen (left dAI). The results of this study support the view that the insula plays a central role in the experience-dependent modulation of sensory integration within the vocal motor system, possibly by optimizing conscious and non-conscious aspects of salience processing associated with singing-related bodily signals.
Xenacoelomorpha : the "simple" key to bilaterian ancestry?

Xenacoelomorpha (comprising Xenoturbellida, Acoela and Nemertodermatida) is a clade of marine worms whose position in the tree of life is still in debate. Several phylogenetic analyses have shown them to be placed at the base of all bilaterian animals (e. g. chordates, arthropods) or at a more derived position as sister group to the Ambulacraria (echinoderms and hemichordates) within the Bilateria. A key characteristic is the absence of traits found in other bilaterian animals. Orthogroups are groups of orthologous genes found in several organisms. Orthologues are assumed to retain the same function. These functions would be specific to the clade where an orthogroup is prevalent. I investigate a method to automatically establish and validate orthogroups specific to Bilateria, Protostomia and Deuterostomia. These genes could be relevant for the clades’ respective emergence and differences. These sets will also help to ascertain what genes/functions are absent from Xenacoelomorpha. MicroRNAs (miRNAs) are small non-coding RNA molecules involved in RNA silencing and post-transcriptional regulation of gene expression. MiRNAs have not been extensively studied in the Xenaceolomorpha. I introduce a fully automatic miRNA detection pipeline to infer and confirm the existence of pre-miRNA sequences in the genome of Xenoturbella bocki as well as predict miRNA candidates from several xenacoel genomes. I report previously undetected miRNA families and opine that previous analyses on Acoelomorpha failed due to loss caused by the higher evolutionary rate when compared to the Xenoturbellida.
The combined effects of hypoxia and fish kairomones on several physiological and life history traits of
 Daphnia

Numerous studies have tested the combined effect of the threat of predation by fish and low oxygen concentrations on the phenotypic plasticity of Daphnia. These studies assessed the trade‐off between minimising predation risk and the negative effects of oxygen deficiencies in the context of depth selection behaviour. We tested whether this trade‐off also affects physiological and life history traits. We expected an interactive effect between the threat of fish predation and low oxygen concentrations, such, that the net effect of both stressors would be antagonistic (lower than the sum of each of the stressors acting separately), rather than additive (or synergistic) on the majority of traits investigated, but we predicted synergistic effects on heat shock proteins (HSPs). To test this, we performed life table experiments in different oxygen concentrations (normoxia and hypoxia) and levels of predation threat (the presence and absence of fish kairomones) on HSP70 and putative HSP110, haemoglobin concentration and life history traits with small‐bodied Daphnia galeata and large‐bodied Daphnia pulex originating from waterbodies where there were different risks of fish predation. As predicted, the net effect of both stressors was antagonistic for most of the physiological and ecological variables studied. The presence of kairomones resulted in decreased body size of adults, egg size, egg size in relation to brood chamber volume, and in increased clutch size in relation to body size. These effects were weaker in hypoxia than in normoxia, which may suggest an existence of adaptive responses caused by a lower perceived risk in hypoxia than in normoxia, as the foraging abilities of fish are limited by oxygen deficiencies. The presence of kairomones hampered the production of haemoglobin in hypoxia for the clones of larger‐bodied species, which suggests the existence of a trade‐off between reduced visibility under positive‐size selective predation risk and increased efficiency of oxygen transport to body tissues. The presence of kairomones and hypoxia resulted in an increased level of putative HSP110, and the effect of kairomones was stronger in hypoxia than in normoxia. More complex results were obtained for the effect of both stressors on the level of HSP70. The findings of our study provide a new insight on the interactions between planktivorous fish and zooplankton in aquatic food webs. More specifically, these findings suggest the existence of unexplored size‐dependent eco‐physiological trade‐offs between minimising predation risk and mitigating the negative effects of oxygen deficiencies.
Scale-resolved analysis of brain functional connectivity networks with spectral entropy

Functional connectivity is derived from inter-regional correlations in spontaneous fluctuations of brain activity, and can be represented in terms of complete graphs with continuous (real-valued) edges. The structure of functional connectivity networks is strongly affected by signal processing procedures to remove the effects of motion, physiological noise and other sources of experimental error. However, in the absence of an established ground truth, it is difficult to determine the optimal procedure, and no consensus has been reached on the most effective approach to remove nuisance signals without unduly affecting the network intrinsic structural features. Here, we use a novel information-theoretic approach, based on von Neumann entropy, which provides a measure of information encoded in the networks at different scales. We also define a measure of distance between networks, based on information divergence, and optimal null models appropriate for the description of functional connectivity networks, to test for the presence of nontrivial structural patterns that are not the result of simple local constraints. This formalism enables a scale-resolved analysis of the distance between an empirical functional connectivity network and its maximally random counterpart, thus providing a means to assess the effects of noise and image processing on network structure. We apply this novel approach to address a few open questions in the analysis of brain functional connectivity networks. Specifically, we demonstrate a strongly beneficial effect of network sparsification by removal of the weakest links, and the existence of an optimal threshold that maximizes the ability to extract information on large-scale network structures. Additionally, we investigate the effects of different degrees of motion at different scales, and compare the most popular processing pipelines designed to mitigate its deleterious effect on functional connectivity networks.