Miracle-dz/UniFAR-FTUs huggingface dataset:
Keratin 1 Plays a Critical Role in Golgi Localization of Core 2 N-Acetylglucosaminyltransferase M via Interaction with Its Cytoplasmic Tail*

Background: The Golgi retention mechanism of core 2 N-acetylglucosaminyltransferase M (C2GnT-M) is not known. Results: Keratin 1 retains C2GnT-M in the Golgi by interacting with its cytoplasmic tail via the rod domain. Conclusion: Keratin 1 is the protein that helps retain C2GnT-M in the Golgi. Significance: Keratin 1 plays a critical role in the regulation of O-glycosylation pathways. Core 2 N-acetylglucosaminyltransferase 2/M (C2GnT-M) synthesizes all three β6GlcNAc branch structures found in secreted mucins. Loss of C2GnT-M leads to development of colitis and colon cancer. Recently we have shown that C2GnT-M targets the Golgi at the Giantin site and is recycled by binding to non-muscle myosin IIA, a motor protein, via the cytoplasmic tail (CT). But how this enzyme is retained in the Golgi is not known. Proteomics analysis identifies keratin type II cytoskeletal 1 (KRT1) as a protein pulled down with anti-c-Myc antibody or C2GnT-M CT from the lysate of Panc1 cells expressing bC2GnT-M tagged with c-Myc. Yeast two-hybrid analysis shows that the rod domain of KRT1 interacts directly with the WKR6 motif in the C2GnT-M CT. Knockdown of KRT1 does not affect Golgi morphology but increases the interaction of C2GnT-M with non-muscle myosin IIA and its transportation to the endoplasmic reticulum, ubiquitination, and degradation. During Golgi recovery after brefeldin A treatment, C2GnT-M forms a complex with Giantin before KRT1, demonstrating CT-mediated sequential events of Golgi targeting and retention of C2GnT-M. In HeLa cells transiently expressing C2GnT-M-GFP, knockdown of KRT1 does not affect Golgi morphology but leaves C2GnT-M outside of the Golgi, resulting in the formation of sialyl-T antigen. Interaction of C2GnT-M and KRT1 was also detected in the goblet cells of human colon epithelial tissue and primary culture of colonic epithelial cells. The results indicate that glycosylation and thus the function of glycoconjugates can be regulated by a protein that helps retain a glycosyltransferase in the Golgi.
Modal Description Logics: Modalizing Roles

We construct a new concept description language intended for representing dynamic and intensional knowledge. The most important feature distinguishing this language from its predecessors in the literature is that it allows applications of modal operators to all kinds of syntactic terms: concepts, roles and formulas. Moreover, the language may contain both local (i.e., state-dependent) and global (i.e., state-independent) concepts, roles and objects. All this provides us with the most complete and natural means for reflecting the dynamic and intensional behaviour of application domains. We construct a satisfiability checking (mosaic-type) algorithm for this language (based on ALC) in (i) arbitrary multimodal frames, (ii) frames with universal accessibility relations (for knowledge) and (iii) frames with transitive, symmetric and euclidean relations (for beliefs). On the other hand, it is shown that the satisfaction problem becomes undecidable if the underlying frames are arbitrary strict linear orders, 〈$$\mathbb{N}$$, <〉, or the language contains the common knowledge operator for n ≥ 2 agents.
No Relation Between Cystic Fibrosis–Related Diabetes and Type 1 Diabetes Autoimmunity

Diabetes is the most common comorbidity in individuals with cystic fibrosis. The etiology is poorly understood. Data on the presence of diabetes autoantibodies are conflicting, and little is known about type 1 diabetes gene associations. Our goal was to determine the prevalence of antibodies and HLA haplotypes known to be associated with type 1 diabetes in cystic fibrosis–related diabetes (CFRD). Patients with CFRD with fasting hyperglycemia were recruited from the University of Minnesota. Serum for antibodies and buffy coats for HLA were sent for analysis to the Barbara Davis Center for Childhood Diabetes (BDC). All patients gave informed consent. The Eisenbarth laboratory at BDC serves as the autoantibody/HLA reference laboratory for large national diabetes studies. Insulin, insulinoma-associated protein 2 (IA-2), GAD65, and zinc transporter 8 (ZnT8) autoantibodies were measured by radioimmunoassay …
Beta Cell Adaptation to Dexamethasone-Induced Insulin Resistance in Rats Involves Increased Glucose Responsiveness but not Glucose Effectiveness

Islet beta cell adaptation to dexamethasone-induced insulin resistance was characterized with respect to glucose-stimulated insulin secretion and islet innervation. Male Sprague-Dawley rats were injected daily with dexamethasone (2 mg/kg for 12 days), which resulted in hyperinsulinemia and hyperglycemia compared with controls (which were injected with sodium chloride). Insulin secretion was characterized in collagenase-isolated islets. Islet innervation was examined by immunocytochemical analysis of tyrosine hydroxylase, neuropeptide Y (sympathetic nerves), and vasoactive intestinal polypeptide (cholinergic nerves). In islets isolated from the insulin-resistant animals, the insulin response to 3.3 or 8.3 mM glucose was three times greater during perifusion compared with controls (p < 0.001). Incubation of islets at 0 to 20 mM glucose revealed a marked leftward shift of the glucose dose–response relation after dexamethasone treatment (potency ratio, 1.78;p < 0.01), with no difference at 0 or 20 mM glucose. Thus, the potency but not the efficacy of glucose was increased. The number of islet nerves did not differ between dexamethasone-treated rats and controls. Dexamethasone-induced insulin resistance leads to adaptively increased glucose responsiveness of the islet beta cells, with increased potency, but not increased efficacy, of glucose to stimulate insulin secretion without any evidence of altered islet innervation.
How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model

The fossil record is a rich source of information about biological diversity in the past. However, the fossil record is not only incomplete but has also inherent biases due to geological, physical, chemical and biological factors. Our knowledge of past life is also biased because of differences in academic and amateur interests and sampling efforts. As a result, not all individuals or species that lived in the past are equally likely to be discovered at any point in time or space. To reconstruct temporal dynamics of diversity using the fossil record, biased sampling must be explicitly taken into account. Here, we introduce an approach that uses the variation in the number of times each species is observed in the fossil record to estimate both sampling bias and true richness. We term our technique TRiPS (True Richness estimated using a Poisson Sampling model) and explore its robustness to violation of its assumptions via simulations. We then venture to estimate sampling bias and absolute species richness of dinosaurs in the geological stages of the Mesozoic. Using TRiPS, we estimate that 1936 (1543–2468) species of dinosaurs roamed the Earth during the Mesozoic. We also present improved estimates of species richness trajectories of the three major dinosaur clades: the sauropodomorphs, ornithischians and theropods, casting doubt on the Jurassic–Cretaceous extinction event and demonstrating that all dinosaur groups are subject to considerable sampling bias throughout the Mesozoic.
Targeted induction of meiotic double-strand breaks reveals chromosomal domain-dependent regulation of Spo11 and interactions among potential sites of meiotic recombination

Meiotic recombination is initiated by programmed DNA double-strand break (DSB) formation mediated by Spo11. DSBs occur with frequency in chromosomal regions called hot domains but are seldom seen in cold domains. To obtain insights into the determinants of the distribution of meiotic DSBs, we examined the effects of inducing targeted DSBs during yeast meiosis using a UAS-directed form of Spo11 (Gal4BD-Spo11) and a meiosis-specific endonuclease, VDE (PI-SceI). Gal4BD-Spo11 cleaved its target sequence (UAS) integrated in hot domains but rarely in cold domains. However, Gal4BD-Spo11 did bind to UAS and VDE efficiently cleaved its recognition sequence in either context, suggesting that a cold domain is not a region of inaccessible or uncleavable chromosome structure. Importantly, self-association of Spo11 occurred at UAS in a hot domain but not in a cold domain, raising the possibility that Spo11 remains in an inactive intermediate state in cold domains. Integration of UAS adjacent to known DSB hotspots allowed us to detect competitive interactions among hotspots for activation. Moreover, the presence of VDE-introduced DSB repressed proximal hotspot activity, implicating DSBs themselves in interactions among hotspots. Thus, potential sites for Spo11-mediated DSB are subject to domain-specific and local competitive regulations during and after DSB formation.
PREVALENCE , CURRENT ANTIBIOGRAM AND RISK FACTORS ASSOCIATED WITH MASTITIS IN DAIRY GOATS IN PUNJAB

The present study was intended to estimate the prevalence of subclinical mastitis (SCM) in apparently healthy dairy goats, to carry out culture sensitivity of isolated pathogens and to elucidate the associated risk factors of mastitis. A total of 200 goats comprising of 397 udder halves from 10 flocks of Punjab was carried out. Milk samples from were collected and screened for California Mastitis Test (CMT), bacteriological examination, and culture sensitivity pattern of the isolated organism. The potential risk factors associated with the occurrence of SCM were analysed using multiple regression and univariable logistic regression analysis. Prevalence of SCM at goat level was 55.5%, and at udder half level it was 46.0%. There was found no significant (p>0.05) difference on the occurrence of SCM between left and right udder halves. Coagulase negative staphylococci were the chief pathogens (75.65%) isolated from infected udder halves. Tetracycline was found to be the most effective drug and penicillin the least. Multiple regression showed that risk factors such as age, parity, milk yield, days in milk and season added significantly (p < 0.001) to the prediction. Univariable logistic regression analysis depicted that mastitis was more prevalent in does with increased age, parity and during the season Nov-Dec.
French College Students’ Sports Practice and Its Relations with Stress, Coping Strategies and Academic Success

College students at university have to face several stress factors. Although sports practice has been considered as having beneficial effects upon stress and general health, few studies have documented its influence on this specific population. The aim of this comparative study was to determine whether the intensity of the college students’ sports practice (categorized into three groups: rare, regular, or intensive) would influence their levels of stress and self-efficacy, their coping strategies, and their academic success/failure. Three self-completion questionnaires were administered to 1071 French freshmen during their compulsory medical visit at the preventive medicine service of the university. Results indicated that students with intensive sport practice reported lower scores of general stress, academic stress, and emotion-focused coping strategies, and higher scores of self-efficacy than those with rare practice. However, the proportion of successful students did not differ significantly between the three groups of sports practice.
Comparison between the Effects of Different Types of Membership Functions on Fuzzy Logic Controller Performance

Membership functions (MFs) are the building blocks of fuzzy set theory, i.e., fuzziness in a fuzzy set is determined by its MF. Accordingly, the shapes of MFs are important for a particular problem since they effect on a fuzzy inference system. They may have different shapes like triangular, trapezoidal, Gaussian, etc. The only condition a MF must really satisfy is that it must vary between 0 and 1. In this paper, a straightforward approach for designing a fuzzy logic based controller is presented to evaluate the effect of membership function in fuzzy logic controller, and presents the performance comparison of fuzzy logic controller with three different types of membership function. An attempt has been made to develop a fuzzy based control system for Antenna Azimuth Position control. This was done using Matlab/Simulink module
Peripheral Neuropathy Associated with Ischemic Vascular Disease of the Lower Limbs

This paper deals with the possible identification of somatic and autonomic nerve damage in patients with peripheral obliterative arterial disease (POAD) at different stages of the disease, with a well-reproducible technique like electroneurographic evaluation of nerve conduction. In 64 patients with intermittent claudication, 19 patients with pain at rest, and 7 patients with trophic ulcers, electroneurographic evaluation of motor (tibial and peroneal) and sensory (superficial peroneal and sural) nerve conduction was performed. The median nerve (motor and sensory) was used as control. A severe impairment of sural and superficial peroneal nerve velocities was evident in many claudicant patients and in all patients with pain at rest and trophic ulcers, with a progression in the conduction abnormalities in advanced stages of the disease. Motor nerve conduction showed only minor reductions in patients with claudica tion and pain at rest, although some of them did show very poor velocity values. In 21 patients with intermittent claudication and sensory nerve abnormalities, the autonomic fibers activity, evaluated by the skin sympathetic response (SSR) test, was significantly depressed, thus suggesting an involvement of the local autonomic system in the ischemic disease. A correlation exists between the severity of the somatic nerve damage and the stage of the vascular insufficiency. However, in the group of claudicant patients, the evidence of similar ischemic threshold (claudication distance) may be associated with a marked difference in the amount of somatic nerve damage. The somatic and autonomic nerve alterations may play a relevant role in the progression of the disease toward critical limb ischemia.
THE RELATIONSHIP OF ACUTE PULMONARY EFFECTS OF ORGANIC MATERIALS TO CHRONIC PULMONARY EFFECTS

HOW does one approach the problem of determining whether exposure to organic material produces pulmonary disease? I believe that the following questions should be asked: 1) Does the exposure in question produce acute pulmonary disease? 2) Does the exposure produce chronic pulmonary disease? 3 ) Are there unique characteristics which make that disease easy to detect and quantify? 4) Does the acute reaction have anything to do with the chronic reaction (if both occur)? 5) Does the former predict the latter? 6) If it does, is the correlation tight enough to permit determination of safe exposure on the basis of acute reactions? or 7) Does the acute reaction reveal the individual worker who is at high risk of developing chronic complications? 8) Is it necessary to have acute reactions for chronic effects to be produced? What seems important, from the standpoint of prevention and control of these diseases, is to gain a much better understanding of the chronic effects of exposure. While the search for the understanding of mechanisms is intriguing, and while the search for better techniques to detect subtle effects may be useful, and while the identification of the etiologic agent is of obvious importance, what we really want to know is the chronic disease potential of these exposures and the safe level of exposure. This is, of course, easier said than done, but I believe that we in the scientific community have the duty and obligation to make strong efforts to answer some of these questions. So far we have not done a very good job. I believe our biggest problem lies in identifying, quantifying and controlling those occupational exposures which may be producing chronic, non-specific, respiratory disease with no special identifying characteristics.
Hemorrhagic infarction: guilt by association?

Efforts to clarify the natural prevalence, radiologic features, and clinical consequences of hemorrhagic infarction (HI), as seen on CT, are welcome. This information is especially important because HI has been viewed as an ominous sign of potential neurologic disaster and has prompted a reluctance to use anticoagulants. More recently, fear of hemorrhagic transformation has raised concern about the risks of using thrombolytic agents in the treatment of acute stroke. In the CT-angiographic report in this issue of the AJNR, Bozzao et al. [1] found that 50% (18/36) of their patients with hemispheric infarcts had HI on the CT scans obtained on the seventh day after stroke. No His were present in any patients on the initial 4-hr CT scan, which is consistent with other reports that HI develops sometime after the first several hours. HI is usually detected by day 3 or 4 but can be found in serial CT studies as late as the second week after stroke [2-5]. The possibility that anticoagulants, given to most of these patients, may have contributed to the large number of His cannot be dismissed entirely, but the doses and duration of treatment were not excessive, and other reports [3, 6-9] of serial CT scans in patients who did not receive anticoagulants have shown a range of HI up to 43%. As expected, autopsy studies [1 0-13] of patients who had embolic strokes showed a higher prevalence of HI; 50-70%, consistent with the more severe nature of the pathologic changes in patients who died. Bozzao et al. have shown that early hypodensity on the initial CT scan obtained within 4 hr of stroke was a predictor of HI in 72% (18/25) of their patients. HI did not develop in any of the remaining 11 who did not have early CT signs of
Eigenvalues of K1,k ‐Free Graphs and the Connectivity of Their Independence Complexes

Let G be a graph on n vertices, with maximal degree d, and not containing K1,k as an induced subgraph. We prove: 1. λ(G)≤(2−12k−2+o(1))d 2. η(I(G))≥n(k−1)d(2k−3)+k−1. Here λ(G) is the maximal eigenvalue of the Laplacian of G, I(G) is the independence complex of G, and η(C) denotes the topological connectivity of a complex C plus 2. These results provide improved bounds for the existence of independent transversals in K1,k ‐free graphs.
Determing Trustworthiness in E-Commerce Customer Reviews

In this paper, we delve into opinion mining and sentiment analysis of customer reviews posted on online e–Commerce portals such as Amazon.com . Speciﬁcally, we look at novel ways of automatic labelling of data for customer reviews by looking at the number of helpful votes and subsequently determine hidden factors that can explain why a customer review is more helpful or trustworthy in contrast to others. We further utilize the factors identiﬁed by Multiple Factor Analysis to training Logistic Regression and Support Vector Machine (SVM) models for classifying reviews into trustworthy and non-trustworthy. Experiments show the effectiveness of our proposed approach.
Cathelicidin Mediates Innate Intestinal Defense against Colonization with Epithelial Adherent Bacterial Pathogens1

Cathelicidin-related antimicrobial peptide (mCRAMP), the sole murine cathelicidin, is encoded by the gene Cnlp. We show that mCRAMP expression in the intestinal tract is largely restricted to surface epithelial cells in the colon. Synthetic mCRAMP had antimicrobial activity against the murine enteric pathogen Citrobacter rodentium, which like the related clinically important human pathogens enteropathogenic Escherichia coli and enterohemorrhagic E. coli, adheres to the apical membrane of intestinal epithelial cells. Colon epithelial cell extracts from Cnlp+/+ mice had significantly greater antimicrobial activity against C. rodentium than those of mutant Cnlp−/− mice that lack mCRAMP. Cnlp−/− mice developed significantly greater colon surface and crypt epithelial cell colonization, surface epithelial cell damage, and systemic dissemination of infection than Cnlp+/+ mice after oral infection with C. rodentium. Moreover, Cnlp+/+ mice were protected from oral infections with C. rodentium inocula that infected the majority of Cnlp−/− mice. These results establish cathelicidin as an important component of innate antimicrobial defense in the colon.
To Memorize or to Predict: Prominence labeling in Conversational Speech

The immense prosodic variation of natural conversational speech makes it challenging to predict which words are prosodically prominent in this genre. In this paper, we examine a new feature, accent ratio, which captures how likely it is that a word will be realized as prominent or not. We compare this feature with traditional accentprediction features (based on part of speech and N -grams) as well as with several linguistically motivated and manually labeled information structure features, such as whether a word is given, new, or contrastive. Our results show that the linguistic features do not lead to significant improvements, while accent ratio alone can yield prediction performance almost as good as the combination of any other subset of features. Moreover, this feature is useful even across genres; an accent-ratio classifier trained only on conversational speech predicts prominence with high accuracy in broadcast news. Our results suggest that carefully chosen lexicalized features can outperform less fine-grained features.
Blind equalization using a tricepstrum-based algorithm

An adaptive blind equalization method is introduced for nonminimum phase communication channels. The method estimates the inverse channel impulse response, by using the complex cepstrum of the fourth-order cumulants (tricepstrum) of the synchronously sampled received signal. As such, the proposed adaptive method depends only on the statistics of the received sequence, and is capable of reconstructing separately both the minimum and maximum phase response of the channel. It is demonstrated, by means of extensive simulations, that the proposed tricepstrum-based equalization scheme performs well and outperforms other existing blind equalizers, at the expense of higher computational complexity. >
The SQALE method for evaluating Technical Debt

This paper presents the SQALE (Software Quality Assessment Based on Lifecycle Expectations) method. We describe its Quality Model and Analysis Model which is used to estimate the Quality and the Technical Debt of an application source code. We provide recommendations and guidelines for using the SQALE indicators in order to analyse the structure and the impact of the Technical Debt.