Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomewide Analysis of Rat Barrel Cortex Reveals Time- and Layer-Specific mRNA Expression Changes Related to Experience-Dependent Plasticity

Because of its anatomical organization, the rodent whisker-to-barrel system is an ideal model to study experience-dependent plasticity. Manipulation of sensory input causes changes in the properties of the barrels at the physiological, structural, and functional levels. However, much less is known about the molecular events underlying these changes. To explore such molecular events, we have used a genomewide approach to identify key genes and molecular pathways involved in experience-induced plasticity in the barrel cortex of adult rats. Given the natural tendency of rats to explore novel objects, exposure to an enriched environment (EE) was used to stimulate the activity of the whisker-to-barrel cortex in vivo. Microarray analysis at two different time points after EE revealed differential expression of genes encoding transcription factors, including nuclear receptors, as well as of genes involved in the regulation of synaptic plasticity, cell differentiation, metabolism, and, surprisingly, blood vessel morphogenesis. These expression differences reflect changes in somatosensory information processing because unilateral whisker clipping showed EE-induced differential expression patterns in the spared versus deprived barrel cortex. Finally, in situ hybridization revealed cortical layer patterns specific for each selected gene. Together, the present study offers the first genomewide exploration of the key genes regulated by somatosensory stimulation in the barrel cortex and thus provides a solid experimental framework for future in-depth analysis of the mechanisms underlying experience-dependent plasticity.
Stunting syndrome in turkeys: physical and physiological changes.

Experiments were conducted to determine the effect of an induced enteric disorder, stunting syndrome (SS), on young turkeys. One-day-old poults were dosed per os with tryptose-phosphate broth (control) or inoculum (inoc) prepared from intestines of SS-affected poults. Inoculation depressed gain (P less than .001) and feed consumption (P less than .001) and impaired (P less than .001) the utilization of feed for gain up to 9 days of age (utilization was 2.02, 2.62 in inoc and 1.27, 1.61 in control poults at 5 and 9 days of age, respectively). Inoculation impaired (P less than .05) retention of nutrients at 8 days of age (dry matter, fat, protein, and ash retentions were 82.5, 88.8, 81.3, and 77.8% in controls and 79.3, 85.6, 74.5, and 74.1% in inoc poults, respectively). Small intestinal weight per 100 g of body weight was greater (P less than .001) in inoc poults, but empty weights per length of jejunum and ileum were less (P less than .05). The jejunal mucosa in inoc poults was thinner, exhibited extensive erosion of villi tips, and had microvilli that seemed to be fused when observed by using scanning electron microscopy. Activities of disaccharidases in the jejunum and ileum of inoc poults were less (P less than .05) than in control poults. In a second experiment, two additional treatments were included, a pair-fed control and a negative control. Control poults pair-fed with the inoc poults grew more rapidly (P less than .01) than inoc poults. The depression in feed consumption due to inoculation accounted for only 54% of the growth depression. Poults inoculated with a suspension prepared from intestines obtained from healthy poults (negative control) performed similarly to controls. Thus, the adverse effects of the SS-inoculum were due to an agent(s) that was present int he intestines of SS-affected poults but not in intestines of healthy poults.
Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation

Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta—CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms.
Effects of pelleted or crumbled diets on the performance and the development of the digestive organs of broilers.

Two types (mash and crumble) of the starter ration (for 0 to 4 weeks of age) and two types (mash and pellets) of the finisher ration (for 4 to 8 weeks of age) were fed to broilers in a 2 X 2 factorial arrangement. Chicks fed the crumbled starter diet gained more weight and consumed more feed (P less than .01). Pelleting the finisher diet also significantly (P less than .01) improved weight gain and feed intake. Feeding the crumble during the starter period significantly (P less than .05) decreased gizzard weight at 4 weeks of age. Pelleting the finisher diet also significantly (P less than .01) reduced weights of the digestive tract and the gizzard at 8 weeks of age, compared to those fed the mash diet.
Endovascular management of inferior vena cava filter thrombotic occlusion

Objective Inferior vena cava occlusion is a potentially life-threatening complication related to caval filters. We present our experience with filter-induced inferior vena cava occlusion in order to assess the feasibility, safety, and effectiveness of endovascular management. Methods A retrospective review of all patients undergoing inferior vena cava filter placement over a 60-month study period was performed. From this cohort, a total of 10 cases of inferior vena cava occlusion after filter placement were identified. Demographics, clinical data, procedures, and outcomes were extracted. Patients were followed to the last clinic visit or until they died. Results One-hundred eighty filters were placed by our group practice during the study period. Of those, a total of 10 patients were identified. Overall, there were 7 males; the mean age was 57.1 years (25–78 years). The median time between inferior vena cava filter placement and filter occlusion was 105 days (range 5–4745 days). All patients were clinically symptomatic at the time of their presentation. Nine out of 10 patients were successfully managed endovascularly. Trellis™-8 thrombectomy was the most common endovascular strategy performed (n = 9). Four patients had balloon angioplasty, two of those with stent placement for chronically occluded inferior vena cava/iliac veins. No thromboembolic complications developed during a median follow-up period of 233 days (range 4–1083 days). Conclusions Endovascular management of inferior vena cava occlusion is feasible, safe, and effective in decreasing thrombus burden in the presence of an inferior vena cava filter. Further studies evaluating long-term inferior vena cava patency and optimal surveillance regimen after endovascular management of filter-related inferior vena cava occlusion are warranted.
How to Evaluate Humorous Response Generation, Seriously?

Nowadays natural language user interfaces, such as chatbots and conversational agents, are very common. A desirable trait of such applications is a sense of humor. It is, therefore, important to be able to measure quality of humorous responses. However, humor evaluation is hard since humor is highly subjective. To address this problem, we conducted an online evaluation of 30 dialog jokes from different sources by almost 300 participants -- volunteers and Mechanical Turk workers. We collected joke ratings along with participants» age, gender, and language proficiency. Results show that demographics and joke topics can partly explain variation in humor judgments. We expect that these insights will aid humor evaluation and interpretation. The findings can also be of interest for humor generation methods in conversational systems.
OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method

In the two transmembrane protein types, outer membrane proteins (OMPs) perform diverse important biochemical functions, including substrate transport and passive nutrient uptake and intake. Hence their 3D structures are expected to reveal these functions. Because experimental structures are scarce, predicted 3D structures are more adapted to OMP research instead, and the inter-barrel residue contact is becoming one of the most remarkable features, improving prediction accuracy by describing the structural information of OMPs. To predict OMP structures accurately, we explored an OMP inter-barrel residue contact prediction method: OMPcontact. Multiple OMP-specific features were integrated in the method, including residue evolutionary covariation, topology-based transmembrane segment relative residue position, OMP lipid layer accessibility, and residue evolution conservation. These features describe the properties of a residue pair in different respects: sequential, structural, evolutionary, and biochemical. Within a 3-residues slide window, a Support Vector Machine (SVM) could accurately determinate the inter-barrel contact residue pair using above features. A 5-fold cross-valuation process was applied in testing the OMPcontact performance against a non-redundant OMP set with 75 samples inside. The tests compared four evolutionary covariation methods and screen analyzed the adaptive ones for inter-barrel contact prediction. The results showed our method not only efficiently realized the prediction, but also scored the possibility for residue pairs reliably. This is expected to improve OMP tertiary structure prediction. Therefore, OMPcontact will be helpful in compiling a structural census of outer membrane protein.
Peer-mentoring Program during the Preclinical Years of Medical School at Bonn University: a Project Description

Introduction: To better prepare young medical students in a thorough and competent manner for the ever increasing clinical, scientific, as well as psychosocial requirements, universities should enable a close, personal transfer of experience and knowledge. Structured mentoring programs are a promising approach to incorporate clinical subjects earlier into the preclinical training. Such a mentoring program facilitates the prioritization of concepts from a broad, theory-heavy syllabus. Here we report the experiences and results of the preclinical mentoring program of Bonn University, which was introduced in the winter semester of 2012/2013. Project desciption: The program is characterized by the concept of peer-to-peer teaching during the preclinical semesters of medical school. Regular, voluntary course meetings with different clinical case examples provide students the opportunity to apply knowledge acquired from the basic science curricula; furthermore, a personal contact for advice and support is ensured. Thus, an informal exchange of experiences is made possible, which provides to the students motivational and learning aids, in particular for the oral examination at the end of the premedical semesters as well as for other examinations during medical school. Results: Over the course of the preceding three years the number of participants and the interest in the program grew steadily. The analysis of collected evaluations confirms very good communication between mentors and students (>80%), as well as consistently good to very good quality and usefulness in terms of the mentors’ subject-specific and other advice. The overall final evaluation of the mentoring program was always good to very good (winter semester: very good 64.8±5.0%, good 35.2±5.0%, summer semester: very good 83.9±7.5%, good 16.1±7.5%) Summary: In summary, it has been shown that the mentoring program had a positive impact on the development, education and satisfaction of students beginning their preclinical semesters at Bonn University.
Development of semi-crystalline polylactide bead foams via liquid CO2 processing

With increasing concerns about the environmental impacts and the sustainability of manufacturing processes and products, biopolymers are currently receiving strong interest as alternatives to petroleum-based polymers. One example is expanded polylactic acid (EPLA) bead foams being developed to replace expanded polystyrene (EPS). A method to convert polylactic acid (PLA) into foamed articles has been developed by the Biopolymer Network Limited (BPN) using liquid carbon dioxide (CO2) as a blowing agent. The technology was initially based on mostly amorphous grades of PLA. The research work presented here aimed at getting a deeper understanding of the CO2-PLA interactions in the BPN process, in particular the effects related to crystallinity. The temperature at which the liquid CO2 impregnation was performed was shown to be the major factor controlling the CO2-induced crystallisation of PLA and the subsequent foaming behaviour. Crystallinity was generally known to strongly affect the foamability of polymers. Three distinct crystallisation regimes, and consequently three foaming regimes, were identified over the whole temperature range spanned by liquid CO2. Impregnation above 10◦C led to the formation of a cohesive network of spherulites in the impregnated PLA which blocked foam expansion. Impregnation between -35 and 10◦C resulted in the formation of smaller dispersed crystals which allowed foaming, but only to high densities for highly crystallisable PLA grades. Impregnation below -35◦C prevented crystallisation and low density foams were produced. This critical impregnation temperature originated from PLA’s initial Tg and the CO2-induced plasticisation of PLA. When impregnation was performed below -35◦C, molecular motion was too limited to allow crystallisation. However, a mesomorphic ordering was observed in PLA. This mesophase melted upon re-heating above Tg and therefore was not detrimental to foaming. Semi-crystalline PLA foamed beads produced after impregnation at -50◦C were successfully moulded into blocks. The mechanical properties of the semi-crystalline foams, tensile strength in particular, were lowered compared to amorphous PLA foams. However, the semi-crystalline foams exhibited high level of crystallinity generated through strain-induced crystallisation during expansion. This provided the foams with enhanced dimensional stability at elevated temperature. At least 15◦C improvement over amor-
A systematic review of the performance of the SEPT9 gene methylation assay in colorectal cancer screening, monitoring, diagnosis and prognosis.

BACKGROUND The applications of the SEPT9 assay are expanding from CRC early diagnosis to screening, therapeutic effect monitoring and prognosis prediction. Its performance in these areas has not been thoroughly examined. OBJECTIVE We aim to evaluate the performance of the SEPT9 assay in CRC screening, diagnosis and therapy by reviewing the current data published in these aspects. METHODS The Ovid MEDLINE, EMBASE, CBMdisc (China Biology Medicine disc) and CJFD (Chinese Journal Full - text Database) database were searched for potential reports on the assay performance. Letters, reviews, meta-analysis and guidelines, basic research studies and articles irrelevant to mSEPT9 detection assays were excluded. Finally, data from 19 studies was summarized and systematically reviewed to clarify the assay performance. RESULTS 2/3 algorithm provided the best overall performance in diagnosis and screening, while the 1/3 algorithm exhibited the best sensitivity in screening. The combination of SEPT9 assay with FIT and/or CEA enhanced the CRC detection rate in screening. The SEPT9 assay appeared to be effective in monitoring the therapeutic effect and may potentially predict the CRC recurrence and survival. CONCLUSION The SEPT9 assay exhibited satisfactory performance in CRC diagnosis and screening, while more evidence is needed for therapeutic effect monitoring and prognosis prediction.
Motion sickness effect in biosignals and body motion disturbance on 4K video viewing

Visual induced motion sickness (VIMS) is one of the most effective factor of visual discomfort on wide screen such as 4K display. Though Biosignal parameter such as LF/HF wasn't reflect the VIMS enough considering individuality, we focus body motion effects that caused by VIMS itself. From the experimental result, the disturbance of body motion reflect time-sequence discomfort and might be possible to estimate the VIMS individuality combining this factors and biosignals.
Research note: sodium and potassium chloride drinking water supplementation effects on acid-base balance and plasma corticosterone in broilers reared in thermoneutral and heat-distressed environments.

One experiment utilizing 188 Vantress x Arbor Acres broilers was conducted to evaluate the effects of isomolar KCl (.5%) and NaCl (.39%) drinking water supplementation on venous pH, PO2, PCO2, HCO3-, hematocrit, and plasma corticosterone as well as rectal temperature and water consumption of broilers reared in heat-distressed and thermoneutral environments. Birds were allotted at 5 wk posthatch into either a thermoneutral (TN; 24 C) or cycling temperature (24 to 35 C) environmental chamber. Heat-distressed (HD) controls had elevated (P less than .05) body temperature (42.9 versus 41.7 C) and PO2 (144.5 versus 108.4 mm Hg). Blood pH, PCO2, and HCO3- (P greater than .1) were not affected by high ambient temperature, but hematocrit (31 versus 32%) for HD controls was reduced (P = .07) compared with TN control birds. At 35 C, drinking water NaCl supplementation decreased (P less than .05) venous PCO2 and HCO3-, increased (P less than .05) PO2, and had no effect on venous pH and water consumption relative to HD controls. Potassium chloride lowered (P = .07) venous pH, decreased (P less than .05) HCO3-, and increased water consumption at 35 C, but PO2 and PCO2 were unaffected relative to HD controls. Heat distress increased (P less than .05) plasma corticosterone by 53%. Sodium chloride failed to impact (P greater than .1) plasma corticosterone but KCl reduced (P less than .05) its concentration during heat distress and increased (P less than .05) bird survivability as compared with heat-distressed controls. The data reported herein suggests that KCl and to a lesser extent NaCl reduces HD consequences by a mechanism as yet undefined.
Are self-reported symptoms of executive dysfunction associated with objective executive function performance following mild to moderate traumatic brain injury?

Background and objective: We examined the relationship between self-reported pre- and post-injury changes in executive dysfunction, apathy, disinhibition, and depression, and performance on neuropsychological tests of executive function, attention/processing speed, and memory in relation to mood levels and effort test performance in individuals in the early stages of recovery from mild to moderate traumatic brain injury (TBI). Method: Participants were 71 noncombat military personnel who were in a semiacute stage of recovery (<3 months post injury) from mild to moderate TBI. Pre- and post-TBI behaviors were assessed with the Frontal Systems Behavior Scale (FrSBe; Grace & Malloy, 2001) and correlated with levels of depressive symptoms, effort test performance, and performance on objective measures of attention, executive function, and memory. Results: Self-reported symptoms of executive dysfunction generally failed to predict performance on objective measures of executive function and memory, although they predicted poorer performance on measures of attention/processing speed. Instead, higher levels of depressive symptomatology best predicted poorer performance on measures of executive function and memory. However, the relationship between memory performance and TBI symptoms was no longer significant when effort performance was controlled. Conclusions: Our findings suggest that, among individuals in early recovery from mild to moderate TBI, self-reported depressive symptoms, rather than patients' cognitive complaints, are associated with objective executive function. However, self-reported cognitive complaints may be associated with objectively measured inattention and slow processing speed.
A Partitioning Algorithm for Extracting Movement Epochs from Robot-Derived Kinematic Data

Point-to-point exercising of the upper-limb, as elicited through the presentation of visual targets on a computer screen, is a ubiquitous paradigm in the robot-assisted rehabilitation of motor-impaired individuals. Kinematic data collected from the robot’s sensors can be used to assess motor function; these data allow objective quantification of motor performance, an approach that shows promise both for guiding therapy and documenting patient progress. It is imperative that these datasets be fully understood, and that tools be continually developed to support analysis and proper interpretation of robot-generated data. It is our experience that data collected from kinematic robots and partitioned according to target achievement may be prone to errors in analysis and interpretation because the movements of highly spastic individuals rarely stop within the target. Here, we propose that it is preferable to partition serial movement data based on local minima in velocity rather than target achievement; this design reflects the convention that movement epochs that start and end at low- or zero-velocity, an assumption that is prevalent even in severely impaired individuals. Using a commercially available robot (MIT-Manus, Interactive Motion Technologies), we recorded movements from 16 moderate- to severely impaired chronic stroke patients. Data partitioned according to target presentation typically interrupted movements mid-motion: velocity at file start was 32.6 ± 26.4% of overall velocity range. By re-apportioning we obtained velocity at file start of 7.4 ± 9.5% of total range. Across 3,200 movements, 12.4 ± 10.4% of data points were re-allocated on average. Thus, our routine is capable of re-partitioning to more accurately reflect observed behavior. Our study is thus the first to identify and propose a solution to the problem of high relevance to the community of robot-aided rehabilitation specialists, i.e. sub-optimal partitioning according to target achievement. Through the algorithm described in this paper, we were able to re-partition the data so that movement epochs were properly demarcated at velocity minima, thus adhering to the fundamental assumptions of human motor behavior, and facilitating analysis of patient performance on a per-movement basis.