Miracle-dz/UniFAR-FTUs huggingface dataset:
Preferential Pharmacological Inhibition of Nav1.6, but not Nav1.1, Abolishes Epileptiform Activity Induced by 4-AP in Mouse Cortical Slices

Brain isoforms of voltage-gated sodium channels (VGSCs) have distinct cellular and subcellular expression patterns as well as functional roles that are critical for normal physiology as aberrations in their expression or activity lead to pathophysiological conditions. In this study, we asked how inhibition of select isoforms of VGSCs alters epileptiform activity to further parse out the roles of VGSCs in the brain. We first determined the relative selectivity of recently discovered small molecule, aryl sulfonamide, inhibitors (ICA-121431 and Compound 801) against Nav1.1, Nav1.2, and Nav1.6 activity using whole-cell patch clamp recordings obtained from HEK293 cells. To test the effects of these inhibitors on epileptiform activity, we obtained multielectrode array (MEA) recordings from mouse cortical slices in the presence of 4-aminopyridine (4-AP) to induce epileptiform activity. We found that the ICA-121431 and Compound 801 compounds are relatively selective for Nav1.1 and Nav1.6, respectively. From the MEA recordings, we found that inhibition of Nav1.6 and Nav1.2 with 500nM of the Compound 801 compound completely abolishes ictal local field potentials induced by 4-AP, whereas inhibition of Nav1.1 with 500nM of the ICA-121431 compound had minimal effect on epileptiform activity induced by 4-AP. Due to the prominent expression of Nav1.1 in inhibitory neurons, we asked whether inhibition of Nav1.1 alone alters activity. We found that, indeed, inhibition of Nav1.1 with the ICA-121431 compound increased basal activity in the absence of 4-AP. These findings expand our current understanding of the roles of VGSC isoforms in the brain and suggest that selective targeting of Nav1.6 may be a more efficacious treatment strategy for epileptic syndromes.
Protein structure search to support the development of protein structure prediction methods

Protein structure prediction is a long-standing unsolved problem in molecular biology that has seen renewed interest with the recent success of deep learning with AlphaFold at CASP13. While developing and evaluating protein structure prediction methods, researchers may want to identify the most similar known structures to their predicted structures. These predicted structures often have low sequence and structure similarity to known structures. We show how RUPEE, a purely geometric protein structure search, is able to identify the structures most similar to structure predictions, regardless of how they vary from known structures, something existing protein structure searches struggle with. RUPEE accomplishes this through the use of a novel linear encoding of protein structures as a sequence of residue descriptors. Using a fast Needleman-Wunsch algorithm, RUPEE is able to perform alignments on the sequences of residue descriptors for every available structure. This is followed by a series of increasingly accurate structure alignments from TM-align alignments initialized with the Needleman-Wunsch residue descriptor alignments to standard TM-align alignments of the final results. By using alignment normalization effectively at each stage, RUPEE also can execute containment searches in addition to full-length searches to identify structural motifs within proteins. We compare the results of RUPEE to mTM-align, SSM, CATHEDRAL and VAST using a benchmark derived from the protein structure predictions submitted to CASP13. RUPEE identifies better alignments on average with respect to RMSD and TM-score as well as Q-score and SSAP-score, scores specific to SSM and CATHEDRAL, respectively. Finally, we show a sample of the top-scoring alignments that RUPEE identified that none of the other protein structure searches we compared to were able to identify. The RUPEE protein structure search is available at https://ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee.
Diet of blue cod, Parapercis colias, living on undisturbed biogenic reefs and on seabed modified by oyster dredging in Foveaux Strait, New Zealand

1. Little has been done to assess the potential impact of habitat modification by bottom fishing gear on the feeding habits of demersal fishes. An analysis is presented of the diet of blue cod in Foveaux Strait, southern New Zealand, based on the gut content of fish taken in winter 1999 from two sites where each site consisted of both undisturbed biogenic reefs and reefs modified by oyster dredging. 2. Of the 420 guts collected, 13% were empty. The overall mean wet weight of gut content was <4 g. No significant habitat or site effects were detected for the proportion of empty guts or the amount of food consumed. 3. A pattern was detected that blue cod on dredged habitats generally fed on more crustaceans than those on undistributed habitats. Blue cod from undisturbed habitat also displayed a more diverse diet than those taken from dredged habitat. These results suggest that long-term disturbance of seabed habitat by the oyster fishery in Foveaux Strait has caused changes to the diet of blue cod. The findings also suggest that actions should be taken to protect the biogenic reefs from further damage if the blue cod fishery and related resources are to be effectively managed. 4. Changes in prey diversity with increasing fish size were also found, with prey diversity (Shannon–Wiener index) increasing from 0.83 to 1.35 over a range of fish size from <25 cm to larger than 34 cm. A total of 52 prey taxa were identified in the diet of blue cod. Crustaceans were the main component, followed by mollusca and polychaeta. Fish, echinodermata and ‘other’ were less important in the diet. Copyright © 2002 John Wiley & Sons, Ltd.
ESTRUTURA E COMPOSIÇÃO DA ICTIOFAUNA DE RIACHOS DO RIO PARANAPANEMA, SUDESTE E SUL DO BRASIL

Seventeen 100 m long streams stretches, none of an order higher than three, were sampled to both sides of the main channel of Rio Paranapanema in the States of Sao Paulo and Parana, southeastern and southern Brazil. Each stream stretch had its midpoint located with a GPS satellite receiver and had its fish fauna sampled via a standardized environmental data and fish collection methodology (primarily utilizing electrofishing) with the aim of providing the following information about each stream: 1) the taxonomic composition of the fish fauna and the contribution of each species in that stream in terms of both number of individuals and biomass; 2) a photographic documentation of the live coloration of representative speci-mens of each collected species; and 3) the description of each sampled environment, with colored photographic illustra-tions and details of the main biotic and abiotic parameters. Overall 3,683 fishes were collected, belonging to six orders, 16 families, 37 genera, and 52 species, with a total biomass of 16.8 kg. Of the collected species, approximately 36% were Siluriformes, 36% Characiformes, 11% Gymnotiformes, 10% Perciformes, 4% Cyprinodontiformes, and 2% Synbranchiformes. The most abundant species in terms of total number of individuals were Astyanax altiparanae (15.2%) and Astyanax sp. 1 (12.3%); The species with the largest biomasses were Astyanax altiparanae (28%) and Geophagus brasiliensis (13%). In terms of abundance and biomass collected for each family, the Characidae was clearly the predominant family followed by the Loricariidae, Pimelodidae, and Cichlidae. Among the sampled stream stretches, locality 14 with 24 species and locality 13 with five species yielded the highest and lowest richness in terms of species numbers, respectively. This coincides with the values obtained for the Shannon-Wienner index of specific diversity (H´ = 0.99 and 0.32, respectively). The median species richness for all streams stretches was 11. In the species richness estimate by extrapolation for all 17 sampled stream stretches, a value of 69 species was obtained (with a standard error of four) indicating the need for an additional moderate sampling effort to reach the asymptote of the curve. Of the 52 collected species, eight (approximately 15% of the total) are clearly new to science and five other species (approximately 10% of the total) are of indefinite taxonomic status and require further analysis. Three of the captured species are introduced (approximately 6% of the total). Analysis of the trophic and spatial structure of the studied fish fauna indicates that the 10 numerically dominant species in the sampled streams can be grouped into four guilds that are in decreasing order of numeric importance: nektonic omnivores; benthonic invertivores; periphytovores; and benthonic omnivores. An identification key for all the species of fish collected during this study it is provided.
Saline-Air Hysterosalpingo–Contrast Sonography Is Equivalent to the Modified Hysterosalpingogram Following Hysteroscopic Sterilization

Purpose To estimate the diagnostic efficacy of saline-air hysterosalpingo–contrast sonography (SA-HyCoSy) compared with the modified hysterosalpingogram (mHSG) for confirmation of both coil location and tubal occlusion following hysteroscopic sterilization. Methods This study included 19 women who underwent both SA-HyCoSy and mHSG where 1 test was followed by the other. Sensitivity, specificity, and positive and negative predictive values for tubal occlusion against the mHSG were calculated for each fallopian tube by 2 independent interpreters. Interrater reliability was assessed using Cohen κ statistic. Procedure time and pain level by 11-point numeric rating scale of SA-HyCoSy and mHSG were also compared. Results Thirty-eight fallopian tubes were evaluated. Tubal occlusion was noted in 97.3% of tubes for both interpreters with the mHSG compared with 92.1% and 94.7% with SA-HyCoSy. The positive and negative predictive values for tubal occlusion were 100%/100% and 50%/33%, respectively, with an overall agreement of 97.4% and 95.7%, κ = 0.48, P < 0.01. Saline-air HyCoSy changed interpretation of coil insert location in 50% and 44.7% for each interpreter, being downgraded from optimal to satisfactory in 42.9% (9/21) and 36% (9/25) and upgraded to optimal in 58.8% (10/17) and 61.5% (8/13), respectively. There were no statistically significant differences in procedural time (7.5 vs 9.4 minutes, P > 0.05) or maximum pain scores (2.3 vs 3.1, P > 0.05) for the mHSG compared with SA-HyCoSy. Conclusions Our findings revealed a high degree of diagnostic accuracy with SA-HyCoSy for tubal occlusion, although coil location changed in nearly half of cases. Avoidance of radiation and patient convenience/compliance with SA-HyCoSy may outweigh the drawbacks.
A field evaluation of cytochrome P4501A as a biomarker of contaminant exposure in three species of flatfish

A study was conducted over the course of a year to determine the induction of hepatic cytochrome P4501A (CYP1A) in three species of benthic fish collected from a contaminated site compared to fish sampled from a less-contaminated site. Juvenile fish were used to minimize effects of reproductive status and migration. CYP1A was determined by two catalytic assays [aryl hydrocarbon hydroxylase (AHH) and ethoxyresorufin O-deethylase (EROD)] and by an immunoassay (ELISA) utilizing polyclonal antibodies raised against purified CYP1A from cod. AHH activities were measured by a standard method (AHH[sub std]) and by two variations of the standard method. All three primary CYP1A measures (AHH[sub std], EROD, and ELISA) showed consistent between-site differences, indicating that induction of CYP1A can be a reliable biomarker of contaminant exposure in fish if appropriate biological variables are controlled for in field studies. Multiple ANOVA demonstrated that the AHH[sub std] and ELISA data showed less variability due to species or temporal differences, and less unexplained variability, compared to the data from the EROD assay or either variation of the AHH assay. For all measures, variability associated with site differences far outweighed species or temporal variability. Immunoassay, while less sensitive than the AHH[sub std] assay, is nonetheless recommendedmore » to be used in conjunction with catalytic assays because of the potential for samples to lose catalytic activity if not handled properly. The current results suggest that the lower noncontaminant-related variability of AHH[sub std] makes this CYP1A measure potentially more useful for monitoring programs in which analysis of trends is a primary goal. « less
Genetic analyses of authentic and alternate forms of Chrysochromulina polylepis (Haptophyta)

Abstract Two motile cell types (authentic and alternate), differing in their organic body scale morphology, were observed in some clonal cultures of Chrysochromulina polylepis Manton et Parke that originated from the 1988 toxic bloom in Skagerrak and Kattegat. Nucleotide sequences from the small subunit ribosomal DNA (18S SSU rDNA) and the first internal transcribed spacer (ITS1) region from several strains of C. polylepis and from other Chrysochromulina species were compared to provide further evidence that both cell types are forms of C. polylepis. Strains of both cell types isolated from Norway were identical in these genomic regions but differed from those of a British strain of C. cf. polylepis and other Chrysochromulina species. Similar fragment lengths were also obtained for both cell types from Norway from PCR amplification of the third intron within a calmodulin gene, but these differed in length from that of the British strain. Our results suggest that both cell types are the same species, incre.
Vocal development and voice breaking in Demoiselle Cranes (Anthropoides virgo)

The vocal development of cranes (Gruidae) has attracted scientific interest due to a special stage, so-called voice breaking. During voice breaking, chicks produce both adult low-frequency and juvenile high-frequency vocalizations. The triggers that affect voice breaking are unknown. For the first time, we study the vocal development of the Demoiselle Crane (Anthropoides virgo). We describe the age and possible drivers of the onset of voice breaking. We analyse the calls of 21 Demoiselle Crane chicks, and compare them with the calls of six adult birds, noting the day when adult low-frequency calls are first recorded as the day when voice breaking begins. The age of voice breaking onset does not depend on hatching date, clutch order or chick body mass. Thus, there is no correlation between body growth and the onset of voice breaking for individual Demoiselle Crane chicks. However, there is a strong relationship between body mass and voice breaking among different crane species. Demoiselle Cranes stop intense body growth at the age of 2 months and start voice breaking at 70 ± 46 days. By way of comparison, Red-crowned Cranes finish the period of intense body growth at the age of 7 months and start voice breaking at 211 ± 60 days. Thus, we show that the Demoiselle Crane has a sudden vocal development, similar to other crane species, and we suggest that the end of intense body growth is the trigger for the onset of voice breaking in cranes.
Symptom expression and ethylene production in leaf blight of cotton caused by Alternaria macrospora and Alternaria alternata alone and in combination

The interaction between the cotton leaf pathogens Alternaria macrospora and Alternaria alternata was studied using dual inoculation at dosages (≈ 103 spores/(mL ∙ pathogen)) that did not produce symptoms with either pathogen alone. This dual inoculation produced the typical disease symptoms (spots and shedding) and disease severity similar to inoculation with 104 spores/mL of A. macrospora alone. Neither pathogen produced ethylene in culture; however, they induced production of ethylene concentrations by diseased tissue that were correlated to both disease severity and leaf shedding. Plants infected by both pathogens produced the highest concentration of ethylene. Leaf discs either from leaves exhibiting symptoms or from symptomless infected leaves produced similarly high concentrations of ethylene. Inoculation of any site of the leaf with A. macrospora alone or with both pathogens resulted in shedding of the leaf. Pretreating inoculated plants with several ethylene inhibitors or an auxin decreased ethyle.
Bioaccumulation of Gold by Filamentous Cyanobacteria Between 25 and 200°C

Plectonema boryanum UTEX 485 was reacted with aqueous AuCl 4 − solutions ( ∼ 2 mM Au) at 25 to 100°C for 1 month, and 200°C for one day. Addition of AuCl4 − to cyanobacteria killed the cultures instantly, and Au was precipitated throughout the cells as nanoparticles. Precipitation of octahedral crystal platelets of Au occurred in the aqueous fluid, with particle size increasing with increase in temperature from about 1.5 μ m at 25°C to 10 μ m at 100°C. Addition of AuCl4 − to suspensions of the dead, autoclaved cyanobacteria also precipitated Au from solution, suggesting that the presence of cell degradation products caused instability of AuCl4 − .
Micellar cholesteric lyotropic liquid crystals

The physico-chemical properties of cholesteric liquid crystals still provide new insights for researchers investigating the structure, local ordering, and phase transitions in condensed matter physics in spite of the fact that they have been known for more than a century. Among cholesterics, the micellar lyotropic cholesteric liquid crystals present outstanding properties which place them in a special category of complex-fluids. One of these key properties is the possibility for changing the micelle shape and shape anisotropy as a function of temperature and/or relative composition of the mixture. Moreover, the existence of polar and nonpolar regions in the lyotropic cholesteric medium, i.e. the loci of the polar heads and hydrocarbon chains of the amphiphilic molecules, respectively, permits a large number of different types of chiral dopants to induce helical structure in the mesophases. Besides this point, the existence of three types of cholesteric phases, originating from the cholesterization of the two uniaxial and one biaxial nematic phases, opens an interesting field of research into fundamental aspects of phase transition and statistical mechanics. In this review, we put together different aspects of the physics of these liquid crystals, from texture observations in a polarized light microscope, to the structure, local ordering, and phase transitions. Some perspectives of new studies are suggested in the concluding remarks.
Thyroid Nodule Malignancy Risk Stratification Using a Convolutional Neural Network

Abstract This study evaluates the performance of convolutional neural networks (CNNs) in risk stratifying the malignant potential of thyroid nodules alongside traditional methods such as American College of Radiology Thyroid Imaging Reporting and Data System (ACR TIRADS). The data set consisted of 651 pathology-proven thyroid nodules (500 benign, 151 malignant) from 571 patients collected at a single tertiary academic medical center. Each thyroid nodule consisted of two orthogonal views (sagittal and transverse) for a total of 1,302 grayscale images. A CNN classifier was developed to identify malignancy versus benign thyroid nodules, and a nested double cross validation scheme was applied to allow for both model parameter selection and for model accuracy evaluation. All thyroid nodules were classified according to ACR TIRADS criteria and were compared with their respective CNN-generated malignancy scores. The best performing model was the MobileNet CNN ensemble with an area under the curve of 0.86 (95% confidence interval, 0.83–0.90). Thyroid nodules within the highest and lowest CNN risk strata had malignancy rates of 81.4% and 5.9%, respectively. The rate of malignancy for ACR TIRADS ranged from 0% for TR1 nodules to 60% for TR5 nodules. Convolutional neural network malignancy scores correlated well with TIRADS levels, as malignancy scores ranged from 0.194 for TR1 nodules and 0.519 for TR5 nodules. Convolutional neural networks can be trained to generate accurate malignancy risk scores for thyroid nodules. These predictive models can aid in risk stratifying thyroid nodules alongside traditional professional guidelines such as TIRADS and can function as an adjunct tool for the radiologist when identifying those patients requiring further histopathologic workup.
Phenotypic selection in a natural population of Impatiens pallida Nutt. (Balsaminaceae)

In the annual plant Impatiens pallida, individuals exhibit a floral heteromorphism consisting of autogamously selfing, cleistogamous (CL) flowers and partially outcrossing, chasmogamous (CH) flowers. As part of an investigation into natural selection and mating system evolution in I. pallida, we measured the magnitude and direction of phenotypic selection on nine life history characters (two traits measured on three dates, one measured on two dates and one measured once). Three of these characters were positively correlated with the ratio of CH/CL flowers produced per plant, which is an important determinant of the mating system. Values for the nine characters and three different measures of fitness (viability, fecundity, lifetime) were estimated for 500 plants in five locations over a single growing season. Based on lifetime fitness, linear selection differentials were significant for all nine characters, indicating a selective advantage to tall, leafy, highly branched plants that flowered early. However, only two of these characters had a direct effect on fitness. Selection was significant on all nine characters when based on fecundity as well as lifetime fitness; however, only three of five characters examined had significant selection based on viability fitness. For all fitness components, the frequency of significant linear and nonlinear selection coefficients was comparable (23% vs 17% of all cases, respectively), but nonlinear coefficients were generally larger. Finally, the magnitude and direction of direct linear selection was heterogeneous among locations, for all characters and all fitness components. Collectively these results suggest that selection is strong, favouring large size, high allocation to reproduction and high CH/CL flower ratios. However, any directional evolutionary changes in vegetative or reproductive characters may be constrained by strong non‐linear and correlational selection.
Effects on shoulder pain and disability of teaching patients with shoulder pain a home-based exercise program: a randomized controlled trial

Objective: To investigate the effect on shoulder pain and disability of teaching patients with shoulder pain how to undertake a home-based exercise program. Design: A randomized controlled trial conducted from September 2015 to January 2016. Setting: Participants’ home. Participants: Sixty participants with shoulder pain who were waiting for physiotherapeutic treatment. Interventions: The control group (n = 30) received minimal education about their shoulder condition and instructions to continue their activities as normal. The intervention group (n = 30) received a two-month home exercise program with one-hour sessions delivered by a physiotherapist to begin and one month after the program for exercise instructions. Main measures: The primary outcome was change in the Shoulder Pain and Disability Index (SPADI). The secondary outcomes included change in the numeric pain rating scale and medication intake for pain relief. Results: The patients’ average age was 54.3 (13.8) years. SPADI scores at baseline were 60.9 (16.5) in the intervention and 64.7 (15.3) in the control group. After two months, the SPADI scores decreased to 18.8 (28.6) and to 61.4 (24.0), respectively, in the intervention and control groups with an estimated mean difference of 40.0, effect size: 1.61. The intervention group showed a reduced pain intensity (estimated mean difference: 3.7, effect size: 2.43) and medication intake (chi-square: 0.001). The number needed to treat was 1.2 for one patient to have a SPADI score <20. Conclusion: Teaching patients with shoulder pain how to undertake a home-based exercise program improved shoulder function and reduced pain intensity and medication intake over two months.