Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrafast Readout of Representations from Spatially Distributed Rodent Hippocampal Field Potentials

Demodulated oscillatory activity at theta frequency band extracted from spatially distributed hippocampal local field potentials (LFPs) encode rodent’s position during maze run. However, it remains unclear how spatial information is encoded in hippocampal field potentials across various immobility and sleep states. Here, we showed that unclustered hippocampal field potential amplitude at ultra-high frequency band (>300 Hz), or known as multiunit activity (MUA), across high-density silicon probe channels provide not only a fast and reliable reconstruction of the rodent’s position in wake, but also a direct readout of replay content during sharp wave ripples (SPW-Rs) in immobility and slow wave sleep. We also employed unsupervised learning approaches to extract low-dimensional MUA features during run and ripple periods, and developed Bayesian methods to infer latent dynamical structures from lower-rank MUA features that were coherent with those derived from clustered spikes. Furthermore, we used an optical flow estimation method to identify propagating spatiotemporal LFP patterns, and derived a set of hippocampal LFP spatiotemporal features for decoding applications. Finally, we developed hybrid forward decoding strategies to predict animal’s future decision at a choice point in goal-directed navigation. Our results point to a robust real-time decoding strategy from large-scale (up to 100,000 electrodes) recordings for closed-loop neuroscience experiments.
A Comparative Study of Antibiotic Sensitivity Pattern of Escherichia coli Isolated from Various Clinical Samples over a Period of 3 Years

Escherichia coli, a gram negative bacillus, is present as a normal flora in human intestine. It is present in hospital environment and is a common cause of nosocomial infection. In recent years it has shown resistance to various groups of antibiotics. We are now having very limited numbers of antibiotics which are effective against Escherichia coli. E. coli is ranked as the most common cause of hospital acquired infection in many hospitals (Berkley et al., 2005).
BIOLOGICAL VALUE OF PUNY FRUITS RELATED TO THEIR ANTIRADICAL ACTIVITY

All analysed species of puny fruits (red currant (Ribes rubrum L) variant Jonkheer van Tets, white currant (Ribes vulgare L.) variant Blanka, black currant (Ribes nigrum L.) variant Eva, blueberry (Vaccinium myrtilis) variant Berkeley, elderberry (Sambucus nigra L.) variant Sambo, hawthorn (Crataegus oxyacantha), mulberry (Morus nigra L.) genotypes M152 and M047) are natural sources of anthocyan pigments and vitamin C with a high antiradical activity. Due to the fact that the highest antiradical activity is not accompanied by the highest content of anthocyans and vitamin C in puny fruits, we suppose that the antiradical activity of plant materials is also connected with the presence of other compounds with antioxidant and antiradical activity. From our results follows that all studied puny fruits with a high antiradical activity increase the antioxidant value of human nutrition and also its prophylactic and medicinal effect.
Arctoparmelia collatolica (Parmeliaceae), a new species from Siberia, Russia

Abstract Arctoparmelia collatolica is described as a species new to science based on morphological, chemical and molecular data. The species is similar to the usnic acid-deficient chemotype of A. centrifuga but differs in the grey-brown to brown upper surface in the central part of the thallus and ivory white to pale brown rhizines. The species contains collatolic acid and its derivatives. Seven secondary lichen substances are reported as new for the genus Arctoparmelia. A key to Arctoparmelia taxa is provided.
Prediction of multiple drug resistant pulmonary tuberculosis against drug sensitive pulmonary tuberculosis by CT nodular consolidation sign

Multidrug-resistant tuberculosis (mdrtb) refers to TB infection resistant to at least two most powerful anti-TB drugs, isoniazid and rifampincin. It has been estimated that globally 3.5% (which can be much higher in some regions) of newly diagnosed TB patients, and 20.5% of previously treated patients had mdrtb. Extensively drug-resistant TB (xdrtb) has resistance to rifampin and isoniazid, as well as to any member of the quinolone family and at least one of the second line injectable drugs: kanamycin, amikacin and capreomycin. xdrtb accounts for 4-20% of mdrtb. Early detection and targeted treatment are priorities for mdrtb/xdrtb control. The suspicion of mdr/xdr -pulmonary TB (mdrptb or xdrptb) by chest imaging shall suggest intensive diagnostic testing for mdrptb/xdrptb. We hypothesize that multiple nodular consolidation (NC) may serve one of the differentiators for separating dsptb vs mdrptb/xdrptb cases. For this study, mdrptb cases (n=310) and XDR-PTB cases (⋂=I58) were from the NIAID TB Portals Program (TBPP) . Drug sensitive pulmonary TB (dsptb) cases were from the TBPP collection (n=112) as well as the Shenzhen Center for Chronic Disease Control (n=111), Shenzhen, China, and we excluded patients with HIV(+) status. Our study shows NC, particularly multiple NCs, is more common in mdrptb than in dsptb, and more common in xdrptb than in mdrptb. For example, 2.24% of dsptb patients, 13.23% of mdrptb patients, and 20.89% of xdrptb patients, respectively, have NCs with diameter >= 10mm equal or more than 2 in number.
Effects of technical noise on bulk RNA-seq differential gene expression inference

Motivation Inconsistent, analytical noise introduced either by the sequencing technology or by the choice of read-processing tools can bias bulk RNA-seq analyses by shifting the focus to the variation in expression of low-abundance transcripts; as a consequence these highly-variable genes are often included the differential expression (DE) call and impact the interpretation of results. Results To illustrate the effects of “noise”, we present simulated datasets following closely the characteristics of a H.sapiens and a M.musculus dataset, respectively, highlighting the extent of technical-noise in both a high inter-individual variability (H. sapiens) and reduced variability (M. Musculus) setup. The sequencing-induced noise is assessed using correlations of distributions of expression across transcripts; analytical noise is evaluated through side-by-side comparisons of several standard choices. The proportion of genes in the noise-range differs for each tool combi-nation. Data-driven, sample-specific noise-thresholds were applied to reduce the impact of low-level variation. Noise-adjustment reduced the number of significantly DE genes and gave rise to convergent calls across tool combinations. Availability The code for determining the sequence-derived noise is available for download from: https://github.com/yry/noiseAnalysis/tree/master/noiseDetection_mRNA; the code for running the analysis is available for download from: https://github.com/sheerind/noise_detection.
DISCRIMINANT ANALYSIS AND CORRELATION BETWEEN MORPHOLOGICAL AND PHYSICOCHEMICAL CHARACTERISTICS OF SOME VARIETIES OF MOROCCAN PRICKLY PEAR

In this study, an analysis was carried on four Moroccan varieties of prickly pear grown at three different regions on three different maturity stages. This study aims at making firstly evaluation of the changes which take place in the morphological and physicochemical characteristics of prickly pear fruits on the three different stages of maturity and secondly detection of the correlation between the different descriptors. Statistical analysis reveals that regardless of the degree of maturity, the parameters of skin thickness and floral receptacle depth have changed significantly from one variety to another. The other physical and physico-chemical parameters (floral receptacle diameter, fruit weight, percentage of pulp, skin, Brix, acidity, sugar, vitamin C and fat content) also varied significantly from one vaiety to another and from one maturity stage to another. The analysis also shows that prickly pears ripen the content elements “fruit weight, pulp weight, Brix, sugar and vitamin C content”, increase skin thickeness and decrease acidity content. In conclusion, it seems that among the 14 physical and physicochemical characteristics of the prickly pears studied, only the “fruit weight" parameter is the most important. In addition, the heavier the fruit, the more pulpy, contains more citric acid, vitamin C and fat.
Temporal β diversity—A macroecological perspective

Issue: Biodiversity change, that is how the taxonomic identities and abundances of species in ecological systems are changing over time, has two facets: temporal α diversity and temporal β diversity. To date, temporal α diversity has received most attention even though compositional shifts in assemblages exceed expectations based on ecological theory. Growing concern about the state of the world’s biodiversity highlights the need for better understanding of the extent, and consequences, of compositional reorganization in ecological systems. Challenges: Most methods of measuring β diversity have been developed in a spatial context. We discuss the additional challenges involved in the assessment of temporal change, summarize existing methodological approaches, highlight the importance of establishing relevant baselines, and identify the need for appropriate null models of temporal β diversity. Given considerable potential for research on the macroecology of temporal β diversity we suggest future directions and challenges. Conclusions: Although data availability remains the main impediment to improved quantification of temporal β diversity at macroecological scales, there are substantial opportunities for improved methodology and theory. Taxonomic β diversity has received most attention, but other dimensions of diversity, including functional and phylogenetic, should be part of integrated assessments of biodiversity change. Future approaches need to be ecologically meaningful and interpretable as well as statistically robust. K E Y W O R D S Anthropocene, baseline change, biodiversity theory, biogeography, compositional shifts, null models, richness, temporal α diversity, temporal β diversity, temporal turnover
Cortical state transitions and stimulus response evolve along stiff and sloppy parameter dimensions, respectively

Previous research showed that spontaneous neuronal activity presents sloppiness: the collective behavior is strongly determined by a small number of parameter combinations, defined as “stiff” dimensions, while it is insensitive to many others (“sloppy” dimensions). Here, we analyzed neural population activity from the auditory cortex of anesthetized rats while the brain spontaneously transited through different synchronized and desynchronized states and intermittently received sensory inputs. We showed that cortical state transitions were determined by changes in stiff parameters associated with the activity of a core of neurons with low responses to stimuli and high centrality within the observed network. In contrast, stimulus-evoked responses evolved along sloppy dimensions associated with the activity of neurons with low centrality and displaying large ongoing and stimulus-evoked fluctuations without affecting the integrity of the network. Our results shed light on the interplay among stability, flexibility, and responsiveness of neuronal collective dynamics during intrinsic and induced activity.
Skeletal and Dental Development Preserve Evidence of Energetic Stress in the Moose of Isle Royale

Food shortages can leave diagnostic, and in the case of the dentition, irreversible changes in mineralized tissue that persist into historical and fossil records. Consequently, developmental defects of tooth enamel might be used to track ungulate population irruption but dental tissue’s capacity for preserving historical population density changes has yet to be investigated in wild populations. We test the ability of enamel defects, mandible and metapodial lengths to track changes in the well-known fluctuating moose population of Isle Royale National Park. Our study demonstrates that 1) a moose density threshold exists on the island above which there is a significant decrease in mandible and metatarsus length and a concomitant increase in enamel hypoplasias, 2) food limitation has a more pronounced effect on male than female skeletal growth, and 3) combined data from tooth enamel hypoplasias and bone lengths reflect the relative density of this ungulate population, and should be broadly applicable to other ungulate osteological samples. Developmental defects in dental enamel were among the highest recorded in a wild population, and even during low-density intervals the population density of Isle Royale moose has been high enough to negatively impact skeletal and dental growth, indicating the comparatively poor health of this century-old ecosystem
Determination of the pKa of the four Zn2+-coordinating residues of the distal finger motif of the HIV-1 nucleocapsid protein: Consequences on the binding of Zn2+

Abstract The nucleocapsid protein NCp7 of human immunodeficiency virus type 1 is characterized by two highly conserved CCHC motifs that bind Zn2+ strongly. To elucidate the striking pH-dependence of the apparent Zn2+-binding constants of these motifs further, we investigated, using 1H NMR, potentiometry and fluorescence spectroscopy, the acid-base properties of the four Zn2+-coordinating residues of (35-50)NCp7, a peptide corresponding to the distal finger motif of NCp7. With the exception of the Hβ2 proton of Cys39, the pH-dependence of the Hβ proton resonances of the three Cys residues and, the Hδ and He resonances of His44 in the apopeptide could be fitted adequately with a single pKa. This suggests that the protonating groups are non-interacting, a feature that was confirmed by a potentiometric titration. The pKa of His44, Cys36, Cys39, and Cys49 in the apopeptide were found to be 6.4, 8.0, 8.8 and 9.3, respectively. Accordingly, the deprotonation is almost sequential and may thus induce a sequential binding of Zn2+ to the four coordinating residues. The high pKa of Cys49 is probably related to the negative charge of the neighboring Asp48. Such a high pKa may be a general feature in nucleocapsid proteins (NCs), since an acidic residue generally occupies the (i − 1) position of the C-terminal Cys residue of single-finger NCs and distal finger motifs in two-finger NCs. Molecular dynamics simulation suggested the formation of a hydrogen bonded network that weakly structured the Cys36-Cys39 segment in the apopeptide. This network depends on the protonation state of Cys36 and may thus explain the biphasic behavior of the pH-dependence of the Cys39 Hβ2 resonance. Finally, the pKa values were used to build up a model describing the coordination of Zn2+ to (35-50)NCp7 at equilibrium. It appears that each protonation step of the coordination complex decreases the Zn2+-binding constant by about four orders of magnitude and that a significant dissociation of Zn2+ from the holopeptide can be achieved in acidic cell compartments.
Ecological and Evolutionary Stochasticity Shape Natural Selection

The distribution of biodiversity depends on the combined and interactive effects of ecological and evolutionary processes. The joint contribution of these processes has focused almost exclusively on deterministic effects, even though mechanisms that increase the importance of random ecological processes are expected to also increase the importance of random evolutionary processes. Here we manipulate the sizes of old field fragments to generate correlated sampling effects for a focal population (a gall maker) and its enemy community. Traits and communities were more variable in smaller patches. However, because of the preference of some enemies for some trait values (gall sizes), random variation in population mean trait values exacerbated differences in community composition. The random distribution of traits and interactions created predictable but highly variable patterns of natural selection. Our study highlights how stochastic processes can affect ecological and evolutionary processes structuring the strength and direction of selection locally and at larger scales.
skin-regeneration-effect-of-adipose-stem-cells

Skin is at the forefront of the body for physical, chemical, biological stress or irritation. Damage to the skin can cause health risks and poor quality of life. Skin regeneration involves almost all cells in the skin, but complete healing of the wound may be impossible. Adipose tissue-derived stem cells (ASCs) may play a role in angiogenesis, modulation of inflammation, extracellular matrix remodeling, and refractory skin wound healing. In skin regeneration, ASCs are provided in the form of enzymatically isolated SVF (cellular SVF), mechanically isolated SVF (tissue SVF), or lipograft. This review will discuss the administration method, clinical implications, and effects of ASCs involved in dermal wound healing. *Correspondence to: Woo Jung Ho, Stem Cell Research Center, Apgujeong Miracle Clinic, Seoul, South Korea, Tel: 82-1588-7013; Fax: 82-2000-7822; E-mail: miracleps77@naver.com
Dietary composition and trophic level of Hypanus marianae (Myliobatiformes: Dasyatidae), captured off Pernambuco coast, Brazil

Hypanus marianae , a stingray endemic to Brazil, inhabits coastal coral reef areas occurring in the landings of artisanal fisheries. The present study aimed to characterize the diet of this species captured off Pernambuco. We obtained 77 stomachs with contents: 52.27% female, 47.72% male. DW ranged from 15 to 37.80 cm mean of 26.53 ± 4.82 cm. Four higher taxonomic prey categories were identified: Arthropoda, Annelida, Chordata and Sipuncula. The most important item in the diet was Polychaeta (40.65% IRI), followed by Leptochela serratorbita (30.35% IRI), suborder Dendrobranchiata (10.18% IRI), order Isopoda (4.19% IRI), and Meiosquilla schmitti (3.56% IRI). H. marianae displays specialized predatory habit (BA = 0.06) primarily based on shrimps (42.36% IRI) and polychaetes (40.65% IRI). There was no significant difference in the diet by sex or in sexual development stages. However, neonates fed on decapods crustaceans (70.68%) and polychaetes (17.09%). For immatures, decapod crustaceans (69.5%) and polychaetes (25.86%) made up most of their diet. The adults feed mainly on polychaetes (62.79%) and crustacean decapods (30.47%), with a slight increase of fish (5.46%). The trophic level (TL) estimated was based on stomach content analysis was 3.66 and estimated on the analysis of stable isotopes being 3.29, which classified the species as a mesopredator.
Paraquat exposure of backpack sprayers in agricultural area in Thailand

Abstract Thai agriculturists heavily used paraquat in agricultural areas to control weed and grasses. This study determined paraquat exposure among backpack sprayers in Thailand and identified determinants of occupational exposure. Breathing zone air and dermal samples were collected from 57 backpack sprayers while spraying. Spot urine samples were collected on the day before spraying, end of spraying event and the next day after spraying. The subjects were interviewed about general demographics, agricultural activities, pesticide application and personal protective equipment used while applying paraquat. Paraquat concentrations in urine samples, air samples and dermal samples were determined by HPLC with a fluorescence detector. The median IQR of urinary paraquat concentrations on the day before spraying, end of spraying event, the next day after spraying were 2.51 (0.81–5.59), 8.23 (3.3–13.73) and 3.48 (1.03–8.19) µg/g creatinine, respectively. Concentrations of air samples and total dermal exposures were 5.15 (2.28–10.12) µg/m3 and 92.66 (34.37–1647.46) µg/hr, respectively. Use of battery powered backpack sprayer and standing upwind effectively reduced inhalation exposures. Wearing a long sleeve shirt, long pants, boots, latex gloves and balaclava could reduce paraquat concentration on dermal exposure among backpack sprayers.
Germination behaviour of
 Conyza bonariensis
 to constant and alternating temperatures across different populations

Conyza bonariensis is one of the most problematic weed species throughout the world. It is considered highly noxious due to its interference with human activities, and especially the competition it poses with economically important crops. This research investigated the temperature requirements for seed germination of four populations of C. bonariensis with distinct origin and the influence of daily alternate temperatures. For this, a set of germination tests were performed in growth chambers to explore the effect of constant and alternate temperatures. Seeds of the four populations (from Lleida, Badajoz and Seville, Spain and Bahía Blanca, Argentina) were maintained at constant temperatures ranging from 5–35oC. The final germination and cardinal temperatures (base, optimum and maximum) of each population were obtained. We also tested the influence of daily alternate temperatures on final germination. To do so, seeds were exposed to two temperature regimes: 5/15, 10/20, 15/25, 20/30 and 25/35oC night/day temperature (intervals increasing 5oC, with constant oscillation of 10oC) and to 18/22, 26/24, 14/26, 12/28 and 10/30oC night/day temperature (intervals with average of 20oC, but increasing the oscillation in 4oC between intervals). In general, all populations behaved similarly, with the highest germination percentages occurring in the optimum temperature range (between 21.7oC and 22.3oC) for both constant and alternate temperatures. In general, climatic origin affected germination response, where seeds obtained from the coldest origin exhibited the highest germination percentage at the lowest temperature assayed. In addition, we observed that the alternate temperatures can positively affect total germination, especially in oscillations that were further from the average optimum temperature (20oC), with high germination percentage for the oscillations of 15/25, 20/30, 18/22, 16/24, 14/26, 12/28 and 10/30oC in all populations. A cc ep te d A rti cl e This article is protected by copyright. All rights reserved. The cardinal temperatures obtained were significantly different across the populations. These results provide information that will facilitate a better understanding of the behaviour of Conyza and improve current field emergence models.
Do Value Added Intellectual Coefficient and Corporate Governance Contribute to Firm's Economic Value Added

This study is about examining the influence of Intellectual Capital and Corporate Governance to EVA. Data used in this study were collected from a sample of 121 consumer goods companies in Indonesia and Malaysia from 2010 to 2017. Panel data multiple regression was performed to examine the research framework. The intellectual capital was measured by VAIC value, while the corporate governance was explained by the audit committee, remuneration board, and auditor quality and tenure. This study found that HCE, SCE, audit committee gender, remuneration size and remuneration gender had no effect on EVA in both Malaysian and Indonesian companies. In contrast, the audit committee size was found to affect the EVA of the companies in both countries. The CEE affected the company value of Malaysian companies while it had no effect on Indonesian companies. Audit quality and audit tenure had a positive effect only on Malaysian companies and none on Indonesian companies. This study used limited variables and a narrow business sector, thus the future research may expand the research model for other types of industries and apply the model in other countries.