Miracle-dz/UniFAR-FTUs huggingface dataset:
Alignment among Normative, Prescriptive, and Descriptive Models of Computer Science Curriculum: The Effect of ABET Accreditation on CS Education

In May and June 2021, the author conducted a survey of the computing and mathematical graduation requirements of 500 Bachelor of Science in Computer Science (BSCS) programs in the U.S. to determine alignment among these requirements and those recommended by ACM/IEEE-CS’s Computer Science Curricula 2013 guidelines and ABET’s Criteria for Accrediting Computing Programs 2021–2022 curricular criterion. Specifically, computing and mathematics credit-hour and course graduation requirements were determined for ABET-accredited and non-accredited BSCS programs within public and private universities. As (i) curricular guidelines are recommendations that do not have to be followed, (ii) curricular accreditation criteria are minimal constraints that may be exceeded, and (iii) non-accredited programs may choose to meet or exceed curricular accreditation criterion, it is possible that graduating computer science students are exposed to similar, or a wide variety, of coursework and associated topics. The survey results presented in this article provide broad answers to these three curricular possibilities. In turn, these results can contribute to future discussions concerning the perceived value of accreditation to students and industry stakeholders, allow educators in computer science departments to compare their curriculum to a large sample of other universities, and provide curricular committees additional insight into how various curricular guidelines are realistically being used.
Nucleosome conformation dictates the histone code

Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized ‘codes’ that are read by specialized regions (reader domains) in chromatin associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP-histone PTM] specificity, and thus decipher the histone code / guide epigenetic therapies. However, this has largely been done using a reductive approach of isolated reader domains and histone peptides, with the assumption that PTM readout is unaffected by any higher order factors. Here we show that CAP-histone PTM interaction is in fact dependent on nucleosome context. Our results indicate this is due to histone tail accessibility and the associated impact on binding potential of reader domains. We further demonstrate that the in vitro specificity of a tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. This necessitates we refine the ‘histone code’ concept and interrogate it at the nucleosome level.
Cell cycle-dependent binding between Cyclin B1 and Cdk1 revealed by time-resolved fluorescence correlation spectroscopy

Measuring the dynamics with which the regulatory complexes of the cell cycle machinery assemble and disassemble is a crucial barrier to our understanding that until now has been difficult to address. This considerable gap in our understanding is due to the difficulty of reconciling biochemical assays with single cell-based techniques, but recent advances in microscopy and gene editing techniques now enable the measurement of protein-protein interaction kinetics in living cells. Here, we apply Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Cross-Correlation Spectroscopy (FCCS) to study the dynamics of the cell cycle machinery, beginning with Cyclin B1 and its binding to its partner kinase Cdk1 that together form the major mitotic kinase. Although Cyclin B1 and Cdk1 are known to bind with high affinity, our results reveal that in living cells there is a pool of Cyclin B1 that is not bound to Cdk1. Furthermore, we provide evidence that the affinity of Cyclin B1 for Cdk1 increases during the cell cycle, indicating that the assembly of the complex is a regulated step. Our work lays the groundwork for studying the kinetics of protein complex assembly and disassembly during the cell cycle in living cells.
Age-related differences in GABA: Impact of analysis technique

Previous research using magnetic resonance spectroscopy (MRS) has indicated that GABA levels decline in multiple brain regions over the course of healthy aging. However, brain atrophy also occurs during healthy aging, and as a result the tissue composition of MRS voxels (i.e., the percentage of grey matter, white matter, and cerebrospinal fluid in the voxel) may also differ between age groups. Many authors therefore argue for applying a correction to GABA estimates in order to control for differences in tissue composition. Here, we use data from a large healthy aging study to investigate the influence of three tissue correction strategies on age-group differences in GABA. We also evaluate the use of different analysis packages and reference metabolites on group differences. A 3T MEGA-PRESS sequence was used to obtain spectra from seven voxels placed in the visual, auditory, and sensorimotor cortex of 58 young adults (aged 18-29 years) and 85 older adults. We obtained several different estimates of GABA concentrations from the spectra using two analysis software packages (Gannet 3.1 and LCModel), three reference metabolites (water, creatine and N-acetylaspartate) and four tissue correction strategies. Young adults consistently demonstrated significantly higher GABA concentrations in the visual, auditory, and sensorimotor cortex when we used an uncorrected GABA estimate referenced either to water or creatine. When uncorrected GABA was referenced to N-acetylaspartate, age-related differences were observed only in the right ventral visual cortex. Similarly, when any of the four tissue corrections were applied to the data, only age-related differences in the left and right ventral visual cortex voxels remained. Correlations between GABA concentration estimates obtained from different software packages were moderate, as were correlations between uncorrected GABA estimates when different baseline metabolites were used. Correlations between all tissue corrections we explored were extremely high. These results confirm that reports of age-related differences in GABA concentrations are driven, at least in part, by changes in tissue composition.
3D bioprinting of an implantable xeno‐free vascularized human skin graft

Bioengineered tissues or organs produced using matrix proteins or components derived from xenogeneic sources pose risks of allergic responses, immune rejection, or even autoimmunity. Here, we report successful xeno-free isolation, expansion, and cryopreservation of human endothelial cells, fibroblasts, pericytes and keratinocytes from a single donor. We further demonstrate the bioprinting of a human skin substitute with a dermal layer containing xeno-free cultured human endothelial cells (EC), fibroblasts, and pericytes in a xeno-free bioink containing human collagen type I and fibronectin layered in a biocompatible polyglycolic acid (PGA) mesh and subsequently seeded with xeno-free human keratinocytes to form an epidermal layer. Following implantation of such bilayered skin grafts on the dorsum of immunodeficient mice, keratinocytes form a mature stratified epidermis with rete ridge-like structures. The ECs and pericytes form human EC-lined perfused microvessels within 2 weeks after implantation, preventing graft necrosis, and eliciting further perfusion of the graft by angiogenic host microvessels. In summary, we describe the fabrication of a bioprinted vascularized bilayered skin substitute under completely xeno-free culture conditions demonstrating feasibility of a xeno-free approach to complex tissue engineering.
Inactivation of B. cereus Spores in Whole Milk and Almond Milk by Novel Serpentine Path Coiled Tube UV-C System

A novel continuous thin-film (1.59 mm) serpentine path coiled tube (SPCT) UV system operating at 254 nm wavelength was designed and compared with flow field distribution of whole milk with helical path coiled tube (HPCT) UV system using computational fluid dynamics. The results revealed efficient velocity magnitude distribution at serpentine bend geometric locations of the SPCT UV system. Further in this study, we evaluated B. cereus Spores inactivation in whole milk (WM) and almond milk (AM) using the developed SPCT UV system. Experimental data showed that > 4 log reduction of spores was achieved after six and ten passes of WM and AM at a flow rate of 70 and 162 mL/min, respectively. The biodosimetry method was used to verify the delivered reduction equivalent fluence (REF) and reported as 33 ± 0.73 and 36.5 ± 1.9 mJ/cm2. We noticed no significant effect on lipid oxidation and volatiles profile (p > 0.05) up to delivered REF of 60 mJ/cm2. This study demonstrated that high levels of inactivation of B. cereus spores could be feasible with minimal impact on product quality by UV-C processing of dairy and non-dairy opaque scattering fluids.
period Translation as a Core Mechanism Controlling Temperature Compensation in an Animal Circadian Clock

The most enigmatic of the canonical properties of circadian clocks is temperature compensation where circadian period length is stable across a wide temperature range despite the temperature dependence of most biochemical reactions. While the core mechanisms of circadian clocks have been well described, the molecular mechanisms of temperature compensation are poorly understood especially in animals. A major gap is the lack of temperature compensation mutants that do not themselves unambiguously affect the temperature dependence of the encoded protein. Here we show that null alleles of two genes encoding components of a complex important for translation of the core clock component period in circadian pacemaker neurons robustly alter the temperature dependence of circadian behavioral period length. These changes are accompanied by parallel temperature dependent changes in oscillations of the PER protein and are consistent with the model that these translation factors mediate the temperature-dependence of PER translation. Consistent with findings from modeling studies, we find that translation of the key negative feedback factor PER plays an instrumental role in temperature compensation.
Perturbations in the Carotenoid Biosynthesis Pathway in Tomato Fruit Reactivate the Leaf-Specific Phytoene Synthase 2

The accumulation of the red carotenoid pigment lycopene in tomato (Solanum lycopersicum) fruit is achieved by increased carotenoid synthesis during ripening. The first committed step that determines the flux in the carotenoid pathway is the synthesis of phytoene catalyzed by phytoene synthase (PSY). Tomato has three PSY genes that are differentially expressed. PSY1 is exclusively expressed in fruits, while PSY2 mostly functions in green tissues. It has been established that PSY1 is mostly responsible for phytoene synthesis in fruits. Although PSY2 is found in the chromoplasts, it is inactive because loss-of-function mutations in PSY1 in the locus yellow flesh (r) eliminate carotenoid biosynthesis in the fruit. Here we demonstrate that specific perturbations of carotenoid biosynthesis downstream to phytoene prior and during the transition from chloroplast to chromoplast cause the recovery of phytoene synthesis in yellow flesh (r) fruits without significant transcriptional changes of PSY1 and PSY2. The recovery of carotenoid biosynthesis was abolished when the expression of PSY2 was silenced, indicating that the perturbations of carotenoid biosynthesis reactivated the chloroplast-specific PSY2 in fruit chromoplasts. Furthermore, it is demonstrated that PSY2 can function in fruit chromoplasts under certain conditions, possibly due to alterations in the plastidial sub-organelle organization that affect its association with the carotenoid biosynthesis metabolon. This finding provides a plausible molecular explanation to the epistasis of the mutation tangerine in the gene carotenoid isomerase over yellow flesh.
Clinical and Functional Outcomes of Patients Receiving Cerebral Reperfusion Therapy: A Stroke Databank Study in Brazil

Objectives Cerebral reperfusion therapy is recommended for the treatment of acute ischemic stroke. However, the outcomes of patients receiving this therapy in middle- and low-income countries should be better defined. This study aimed to evaluate the clinical and functional outcomes of cerebral reperfusion therapy in patients with ischemic stroke. Materials and Methods This retrospective study included patients with ischemic stroke treated with cerebral reperfusion therapy, including intravenous thrombolysis (IVT), mechanical thrombectomy (MT), and IVT with MT. The primary outcomes were death and disability, assessed using the modified Rankin scale (mRS), and stroke severity, assessed using the National Institutes of Health Stroke Scale (NIHSS), after intervention and 90 days after ictus. The association between the type of treatment and the primary outcome was assessed using binary logistic regression after adjusting for confounding variables. Furthermore, receiver operating characteristic (ROC) curves were generated to identify the cutoff point of the NIHSS score that could best discriminate the mRS score in all types of treatments. Results Patients (n = 291) underwent IVT only (n = 241), MT (n = 21), or IVT with MT (n = 29). In the IVT with MT group, the incidence of death within 90 days increased by five times (OR, 5.192; 95% CI, 2.069–13.027; p = 0.000), prevalence of disability increased by three times (OR, 3.530; 95% CI, 1.376–9.055; p = 0.009) and NIHSS score increased after IVT (from 14.4 ± 6.85 to 17.8 ± 6.36; p = 0.045). There was no significant difference between the initial NIHSS score and that after MT (p = 0.989). Patients' NIHSS score that increased or decreased by 2.5 points had a sensitivity of 0.74 and specificity of 0.65, indicating severe disability or death in these patients. Conclusion Altogether, a 2.5-point variation in NIHSS score after reperfusion is an indicator of worse outcomes. In our particular context, patients receiving the combination of IVT and MT had inferior results, which probably reflects challenges to optimize MT in LMIC.
Integrated Analysis of Multi-Omics Alteration, Immune Profile, and Pharmacological Landscape of Pyroptosis-Derived lncRNA Pairs in Gastric Cancer

Background: Recent evidence demonstrates that pyroptosis-derived long non-coding RNAs (lncRNAs) have profound impacts on the initiation, progression, and microenvironment of tumors. However, the roles of pyroptosis-derived lncRNAs (PDLs) in gastric cancer (GC) remain elusive. Methods: We comprehensively analyzed the multi-omics data of 839 GC patients from three independent cohorts. The previous gene set enrichment analysis embedding algorithm was utilized to identify PDLs. A gene pair pipeline was developed to facilitate clinical translation via qualitative relative expression orders. The LASSO algorithm was used to construct and validate a pyroptosis-derived lncRNA pair prognostics signature (PLPPS). The associations between PLPPS and multi-omics alteration, immune profile, and pharmacological landscape were further investigated. Results: A total of 350 PDLs and 61,075 PDL pairs in the training set were generated. Cox regression revealed 15 PDL pairs associated with overall survival, which were utilized to construct the PLPPS model via the LASSO algorithm. The high-risk group demonstrated adverse prognosis relative to the low-risk group. Remarkably, genomic analysis suggested that the lower tumor mutation burden and gene mutation frequency (e.g., TTN, MUC16, and LRP1B) were found in the high-risk group patients. The copy number variants were not significantly different between the two groups. Additionally, the high-risk group possessed lower immune cell infiltration abundance and might be resistant to a few chemotherapeutic drugs (including cisplatin, paclitaxel, and gemcitabine). Conclusion: PDLs were closely implicated in the biological process and prognosis of GC, and our PLPPS model could serve as a promising tool to advance prognostic management and personalized treatment of GC patients.
Brain Atrophy and Clinical Characterization of Adults With Mild Cognitive Impairment and Different Cerebrospinal Fluid Biomarker Profiles According to the AT(N) Research Framework of Alzheimer’s Disease

Introduction This study aimed to evaluate, in adults with mild cognitive impairment (MCI), the brain atrophy that may distinguish between three AT(N) biomarker-based profiles, and to determine its clinical value. Methods Structural MRI (sMRI) was employed to evaluate the volume and cortical thickness differences in MCI patients with different AT(N) profiles, namely, A−T−(N)−: normal AD biomarkers; A+T−(N)−: AD pathologic change; and A+T+(N)+: prodromal AD. Sensitivity and specificity of these changes were also estimated. Results An initial atrophy in medial temporal lobe (MTL) areas was found in the A+T−(N)− and A+T+(N)+ groups, spreading toward the parietal and frontal regions in A+T+(N)+ patients. These structural changes allowed distinguishing AT(N) profiles within the AD continuum; however, the profiles and their pattern of neurodegeneration were unsuccessful to determine the current clinical status. Conclusion sMRI is useful in the determination of the specific brain structural changes of AT(N) profiles along the AD continuum, allowing differentiation between MCI adults with or without pathological AD biomarkers.
Lycium barbarum Polysaccharides as Antibiotic Substitutes Improve Growth Performance, Serum Immunity, Antioxidant Status, and Intestinal Health for Weaned Piglets

The aim of the present study is to investigate the effects of dietary Lycium barbarum polysaccharides (LBPs) supplementation on the growth performance, immune response, serum antioxidant status, and intestinal health of weaned piglets. In total, 24 crossed healthy weaned piglets [Duroc × (Yorkshire × Landrace)], of similar body weight (7.47 ± 0.22 kg), were randomly allocated to three treatment groups: CON (basal diet); LBPs (basal diet plus 4,000 mg/kg LBPs); and antibiotic (ABO, basal diet plus 20 mg/kg flavomycin and 50 mg/kg quinocetone). There were eight pigs per group. The study lasted 28 days. When compared with CON, LBPs or ABO dietary supplementation increased average daily gain (P < 0.05), decreased the ratio of feed to gain and the diarrhea ratio (P < 0.05). Similarly, when compared with CON, LBPs dietary supplementation increased serum immunoglobulin G, immunoglobulin M, interleukin-10, interleukin-2, and tumor necrosis factor-α levels (P < 0.05). Dietary LBPs enhanced the activity of serum total antioxidant capacity and glutathione peroxidase, and decreased malondialdehyde levels (P < 0.05). Principal component analysis showed a distinct separation between CON and LBPs groups, but no differences between ABO and LBPs groups. LBPs addition increased Lactobacillus and Faecalibacterium (P < 0.05) levels, while it decreased Enterococcaceae and Enterobacteriaceae (P < 0.05) levels. Furthermore, when compared with the CON group, LBPs increased villus height (P < 0.05) and the villus height to crypt depth ratio in the duodenum and jejunum (P < 0.05). Thus, dietary supplementation with LBPs improved growth performance, antioxidant capacity and immunity, regulated intestinal microbial composition, and may be used as an efficient antibiotic alternative in weaned piglet feed.
Inhibitors of Human Neuraminidase Enzymes Block Transmigration in vitro

Cell migration to a site of inflammation is an important step of the immune response. This process is coordinated by cytokines, receptors, and the signal processing machinery of the cell. Many cellular receptors are glycosylated, and their activity can be modulated through changes in glycan structure. Furthermore, glycosylation can be critical to the folding and trafficking of receptors. In this work, we investigated the role of native human neuraminidase enzymes (NEU) in transmigration. We used a cultured T cell line (Jurkat) and a transwell assay with fibronectin (FN) coated wells and cytokines (IL-4 and TNF-α) as chemoattractants in the bottom chamber. We observed that NEU1, NEU3, and NEU4 were positive regulators of transmigration using an siRNA knockdown. Furthermore, we found that pharmacological inhibition of these enzymes inhibited transmigration. We conclude that human NEU isoenzymes NEU1, NEU3, and NEU4 can act as positive regulators of transmigration and should be investigated as targets for anti-inflammatory strategies.
Physiological Indicators and Production Performance of Dairy Cows With Tongue Rolling Stereotyped Behavior

Non-nutritive oral behaviors, especially tongue rolling, are prevalent in the stabled cow population. These behaviors mean that the environment or management process might not suit the cows, suggesting low welfare. However, few researches have reported the physiological indicators or production performance of dairy cows with the stereotyped behavior. This study aimed to determine physical conditions, daily activity, rumen fermentation, and milk production of cows with tongue-rolling behavior. Three hundred and fifty nine Holstein cows in the same barn and lactation stage were subjected to scan sampling behavior observations 126 times for 7 days. Ten cows with high-frequency tongue-rolling behavior (TON) and 10 cows without abnormal oral behavior (CON) were selected for further study. Serum sample, ruminal fluid, milk sample, and behavior record video of TON and CON cows were collected. TON cows had more drinking behavior and more stable lying behavior than the CON cows during the daytime. The body condition score of the TON cows decreased, while the milk yield, yield of milk fat, protein, and lactose in the study period increased. The TON cows had lower ruminal fluid pH, acetate/propionate ratio, and total volatile acid. The bacterial diversity in the ruminal fluid was not different between the two groups. Compared to CON cows, the TON cows had a higher level of serum stress indicators, such as cortisol, thyroid hormone, and norepinephrine, which positively correlated to the frequency of tongue-rolling behavior. Meanwhile, the TON cows had a higher level of lactate dehydrogenase, serum glucose, total triglyceride, total cholesterol, and Interleukin 6. Overall, it means they suffer from higher levels of stress and have higher energy metabolism for a long time when cows show tongue-rolling behavior. TON cows had suffered a higher stress level and had higher energy metabolic status for a long time. The TON cows might have better heat tolerance to the thermal environment by more lying and drinking time. Our data revealed the changes in milk production, physiological stress indicators of dairy cows with high-frequency tongue rolling behavior, which will provide essential knowledge for the in-depth understanding of tongue rolling behavior in dairy cows.