Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of changes in nutritional demand on gastrointestinal parasitism in lactating rats

Lactating rats experience a breakdown of immunity to parasites, i.e. they carry larger worm burdens after re-infection compared to their non-lactating counterparts. Feeding high-protein foods to lactating rats results in reduced worm burdens. This could be attributed to changes in gastrointestinal environment or to overcoming effects of nutrient scarcity on host immunity. The latter hypothesis was addressed through a manipulation of nutrient demand by manipulating litter size. Twenty-three rats were immunized prior to mating and re-infected on day 2 of lactation with 1600 infective Nippostrongylus brasiliensis larvae. From parturition onwards, rats received ad libitum a low-protein food (100 g crude protein/kg). Litter sizes were standardised to nine (LS9), six (LS6) or three (LS3) pups, by day 2 of lactation. After a further 10 d, LS9 and LS6 rats carried more worms than LS3 rats. However, feeding treatments did not affect concentrations of mucosal inflammatory cells. Achieved feed intake did not differ consistently between the treatment groups. However, LS9 and LS6 rats lost weight, whilst LS3 rats gained weight during lactation. The results support the view that resistance to N. brasiliensis is sensitive to changes in nutrient demand, and the improved resistance to N. brasiliensis is likely due to effects of overcoming nutrient scarcity on host immunity.
Utilizing Hardware Culture in a Case of Atypical Keratitis

Abstract This case report describes the diagnosis and management of a 22-year-old male soft contact lens wearer, who presented with an atypical corneal ulcer in the right eye. The patient presented with a one-day history of significant eye pain, photophobia, and multiple pseudodendritic lesions on the cornea with stromal infiltrate; the differential remained broad. The management was guided by the culture of hardware of the patient’s contact lenses, which grew aspergillus only in the affected contact. In cases where corneal culture is negative, multiple organisms have been isolated from the corneal culture, or in cases where there is no response to medical treatment, culture of hardware may be a useful methodology for isolating the offending microbe in infectious corneal ulcers.
Around or across the Carpathians: colonization model of the Danube basin inferred from genetic diversification of stone loach (Barbatula barbatula) populations

Despite increasing information about postglacial recolonization of European freshwater systems, very little is known about pre‐Pleistocene history. We used data on the recent distribution and phylogenetic relationships of stone loach mitochondrial lineages to reconstruct the initial colonization pattern of the Danube river system, one of the most important refuges for European freshwater ichthyofauna. Fine‐scale phylogeography of the Danubian populations revealed five highly divergent lineages of pre‐Pleistocene age and suggested the multiple origin of the Danubian stone loach. The mean sequence divergence among lineages extended from 7.0% to 13.4%, which is the highest intraspecific divergence observed so far within this river system. Based on the phylogeographical patterns, we propose the following hypothesis to relate the evolution and dispersal of the studied species with the evolution of the Danube river system and the Carpathian Mountains: (i) during the warmer period in the Miocene, the areas surrounding the uplifting Alps and Carpathians served as mountainous refuges for cold‐water adapted fish and promoted the diversification of its populations, and (ii) from these refuges, colonization of the emerging Danube river system may have taken place following the retreat of the Central Paratethys. Co‐existence of highly divergent mtDNA lineages in a single river system shows that range shifts in response to climatic changes during the Quaternary did not cause extensive genetic homogenization in the stone loach populations. However, the wide distribution of some mtDNA lineages indicates that the Pleistocene glaciations promoted the dispersal and mixing of populations through the lowlands.
Detection of protein and mRNA of various components of the NADPH oxidase complex in an immortalized human chondrocyte line.

The immortalized human chondrocyte cell line C-20/A4 has the ability to produce superoxide constitutively at low levels of 5.4 x 10(-2) nmol/min/10(6) cells (S.E.M. = +/-0.5, n = 30) and at raised levels upon stimulation with ionomycin and phorbol 12-myristate 13-acetate. Priming and anti-priming effects of interleukin (IL)-1 beta and IL-4, respectively, are also demonstrated. Reverse transcriptase polymerase chain reaction (RT-PCR) amplification using oligonucleotide primers to components of the NADPH oxidase enzyme complex showed mRNA expression of p22-phox, p40-phox and p47-phox. Western blot analysis using polyclonal antisera indicated the presence of the p47-phox p67-phox polypeptide components. These results show that the C-20/A4 cells contain an NADPH oxidase-like complex, similar to that found in other cell types, which produces superoxide anions.
Eleven Years of Parotid Gland Surgery in a Plastic and Reconstructive Department

Background:Salivary gland tumors are an uncommon entity, comprising 3% to 6% of all head and neck tumors. Approximately 75% to 80% occur in the parotid gland, and 80% are benign. It is difficult to establish epidemiologic characteristics of parotid gland tumors due to their low incidence. We performed a retrospective study to analyze clinical diagnostic and therapeutic features of patients submitted to parotid gland surgery. Methods:A retrospective study was performed, regarding all the patients (n = 96) submitted to surgery for treatment of parotid gland disease in the Department of Plastic and Reconstructive Surgery of Centro Hospitalar de S. João (Porto, Portugal) between 2002 and 2012. Medical records were analyzed and the following data were collected: patient age at diagnosis, sex, tumor location, symptom, tumor position, preoperative diagnosis techniques, type of operation performed, pathology, postoperative complications, adjuvant therapy (radiotherapy or chemotherapy), follow-up time, and tumor recurrence. SPSS was used for statistical analysis. Results:Fifty-two percent of the patients were males and 48% females and mean age of 52.02. In 68.75% of the patients, superficial parotidectomy was performed. Benign pathology was found in 72% patients, and pleomorphic adenoma the most common tumor (39%). Facial paralysis (41.7%), Frey syndrome (9.4%), and great auricular nerve hyposthesia (10.4%) were major complications. Tumor recurrence was observed in 16 patients (16.7%), which forced 17 reoperations (17.7%). There were 5 deaths (5.2%). Conclusion:For most tumors, superficial parotidectomy is an effective treatment with acceptable morbidity. In patients of malignancy, treatment should be aggressive.
The modest outcome of clinical trials with bone marrow cells for myocardial repair: is the autologous source of cells the prime culprit?

Re-entry of cardiomyocytes into cell cycle and participation of the resident cardiac stem cells (CSCs) as part of the intrinsic repair process have been evidenced in the ischemic heart (1-3). Nevertheless, the inadequacy of these mechanisms of intrinsic repair necessitates outside intervention especially when the damage inflicted is massive in terms of the loss of functional myocytes. The situation is further aggravated by the advanced age of the patients with ischemic heart disease, and the complexity of the disease process which renders the tissue environment in the diseased heart more intimidating for the transplanted cells besides impacting the stemness characteristics and reparability of the intrinsically available stem cells (4).
A Cahn-Hilliard equation with a proliferation term for biological and chemical applications

In this paper, we are interested in the study of the solution to a generalization of the Cahn-Hilliard equation endowed with Neumann boundary conditions. This model has, in particular, applications in biology and in chemistry. We show that the solutions blow up in finite time or exist globally in time. We further prove that the relevant, from a biological and a chemical point of view, solutions converge to a constant as time goes to infinity. We finally give some numerical simulations which confirm the theoretical results.
Differentially Methylated Epiloci Generated from Numerous Genotypes of Contrasting Tolerances Are Associated with Osmotic-Tolerance in Rice Seedlings

DNA methylation plays an essential role in plant responses to environmental stress. Since drought develops into a rising problem in rice cultivation, investigations on genome-wide DNA methylation in responses to drought stress and in-depth explorations of its association with drought-tolerance are required. For this study, 68 rice accessions were used for an evaluation of their osmotic-tolerance related to 20% PEG6000 simulated physiological traits. The tolerant group revealed significantly higher levels of total antioxidant capacity and higher contents of H2O2 in both normal and osmotic-stressed treatments, as well as higher survival ratios. We furthermore investigated the DNA methylation status in normal, osmotic-stressed, and re-watering treatments via the methylation-sensitive amplification polymorphism (MSAP). The averaged similarity between two rice accessions from tolerant and susceptible groups was approximately 50%, similar with that between two accessions within the tolerant/susceptible group. However, the proportion of overall tolerance-associated epiloci was only 5.2% of total epiloci. The drought-tolerant accessions revealed lower DNA methylation levels in the stressed condition and more de-methylation events when they encountered osmotic stress, compared to the susceptible group. During the recovery process, the drought-tolerant accessions possessed more re-methylation events. Fourteen differentially methylated epiloci (DME) were, respectively, generated in normal, osmotic-stressed, and re-watering treatments. Approximately, 35.7% DME were determined as tolerance-associated epiloci. Additionally, rice accessions with lower methylation degrees on DME in the stressed conditions had a higher survival ratio compared to these with higher methylation degrees. This result is consistent with the lower DNA methylation levels of tolerant accessions observed in the stressed treatment. Methylation degrees on a differentially methylated epilocus may further influence gene regulation in the rice seedling in response to the osmotic stress. All these results indicate that DME generated from a number of genotypes could have higher probabilityies for association with stress-tolerance, rather than DME generated from two genotypes of contrasting tolerance. The DME found in this study are suspected to be good epigenetic markers for the application in drought-tolerant rice breeding. They could also be a valuable tool to study the epigenetic differentiation in the drought-tolerance between upland and lowland rice ecotypes.
Functional magnetic resonance imaging of real and sham acupuncture. Noninvasively measuring cortical activation from acupuncture.

In Western society, acupuncture is becoming a popular alternative for medical treatment—as evidenced by the 15 million Americans who have reported treatment with that procedure in a single year. The World Health Organization (WHO) reported that there are approximately 10,000 acupuncture specialists in the United States, and an estimated 3,000 practicing acupuncturists are physicians [1]. A scientific understanding of the neuroanatomical regions involved in acupuncture treatment has not been completely developed but will likely be necessary for the increased acceptance of acupuncture by the Western medical community.
Meta-Analysis of the Association between Mir-196a-2 Polymorphism and Cancer Susceptibility

Objective MicroRNA plays a vital role in gene expression, and microRNA dysregulation is involved in carcinogenesis. The miR-196a-2 polymorphism rs11614913 is reportedly associated with cancer susceptibility. This meta-analysis was performed to assess the overall association of miR-196a-2 with cancer risk. Methods A total of 27 independent case-control studies involving 10,435 cases and 12,075 controls were analyzed for the rs11614913 polymorphism. Results A significant association was found between rs11614913 polymorphism and cancer risk in four genetic models (CT vs. TT, OR=1.15, 95%CI=1.05–1.27; CC vs. TT, OR=1.23, 95%CI=1.08–1.39; Dominant model, OR=1.17, 95%CI=1.06–1.30; Additive model, OR=1.08, 95%CI=1.01–1.14). In the subgroup analysis of different tumor types, the C allele was associated with increased risk of lung, breast, and colorectal cancer, but not with liver, gastric, or esophageal cancer. In the subgroup analysis by ethnicity, a significantly increased risk of cancer was found among Asians in all genetic models, but no associations were found in the Caucasian subgroup. Conclusions The meta-analysis demonstrated that the miR-196a-2 polymorphism is associated with cancer susceptibility, especially lung cancer, colorectal cancer, and breast cancer among Asian populations.
Optimal wake-up mechanism for single base station with sleep mode

Base station (BS) sleeping is an effecting way to improve the energy-efficiency of cellular networks. Considering BS sleep mode operation under different scenarios, we focus on three wake-up policies: single vacation (SV) policy, multiple vacation (MV) policy and N policy. A hysteresis time is also considered to avoid frequent BS mode-changing operation. By modeling the systems as M/G/1 vacation queues, we derive two performance measures of interest, expected system response time and energy consumption per bit. The impacts of sleep mode operation parameters and setup time are also studied. In order to determine the optimal parameter settings, which allows for a flexible tradeoff between energy-efficiency and mean delay, a two-step optimization method is proposed. We numerically analyze and investigate the energy-delay tradeoff for different policies, and find that both the MV policy and the N policy have better performance than the SV policy if the sniffing cost is not considered. However, these advantages diminish when the sniffing cost increases.
Heegaard splittings of knot exteriors

The goal of this paper is to offer a comprehensive exposition of the current knowledge about Heegaard splittings of exteriors of knots in the 3-sphere. The exposition is done with a historical perspective as to how ideas developed and by whom. Several new notions are introduced and some facts about them are proved. In particular the concept of a 1/n-primitive meridian. It is then proved that if a knot K in S^3 has a 1/n-primitive meridian; then nK = K#. #K, n-times has a Heegaard splitting of genus nt(K) + n which has a 1-primitive meridian. That is, nK is mu-primitive.
Outcomes of Self-Expanding Metal Stents in Malignant Colonic Obstruction are Independent of Location or Length of the Stenosis: Results of a Retrospective, Single-Center Series

Aim: To evaluate the length and location of stenosis in the colon as predictors of technical and clinical outcomes of stent placement in patients presenting with obstructive colorectal cancer. Methods: A prospective single-center cohort study of patients treated with a colonic stent for malignant obstruction, regardless of stenosis length or location. Stenosis length was assessed globally on the appropriate CT slice as well as by 3D CT reconstruction. We analyzed whether outcomes were different in patients with a right sided-tumor and/or a stenosis >4 cm long. Results: One hundred forty-one patients were evaluated, 63 with a stenosis >4 cm, 48 with a stenosis proximal to the splenic flexure. Technical failure (n = 9) was mainly caused because of looping or due to the difficulty in engaging the stenosis precluding analysis of the relation between the stenosis length and technical success. Both measurement methods showed good agreement. Clinical outcomes were not associated with stenosis length or location. Conclusion: Clinical outcomes of stenting did not differ between groups regardless of stenosis length or location. Measuring stenosis length more precisely using 3D CT reconstructions is not of help.
Hepatotoxicity induced by antifungal drugs itraconazole and fluconazole in rats: a comparative in vivo study

Itraconazole and fluconazole are oral antifungal drugs, which have a wide spectrum antifungal activity and better efficacy than the older drugs. However, both drugs have been associated with hepatotoxicity in susceptible patients. The mechanism of antifungal drug-induced hepatotoxicity is largely unknown. Therefore, the aim of this present study was to investigate and compare the hepatotoxicity induced by these drugs in vivo. Rats were treated intraperitoneally with itraconazole or fluconazole either single (0, 10, l00 and 200 mg/kg) or subchronic (0, 10, 50 and loo mg/kg per day for 14 days) doses. Plasma and liver samples were taken at the end of the study. A statistically significant and dose dependent increase of plasma alanine aminotransferase (ALT) and alkaline phosphatase (ALP) activities were detected in the subchronic itraconazole-treated group. In addition, dose-dependent hepatocellular necrosis, degeneration of periacinar and mizonal hepatocytes, bile duct hyperplasia and biliary cirrhosis and giant cell granuloma were observed histologically in the same group. Interestingly, fluconazole treated rats had no significant increase in transaminases for both single and subchronic groups. In the subchronic fluconazole treated rats, only mild degenerative changes of centrilobular hepatocytes were observed. These results demonstrated that itraconazole was a more potent hepatotoxicant than fluconazole in vivo in rats.
A highly abnormal massive star mass function in the Orion Nebula cluster and the dynamical decay of trapezium systems

The Orion Nebula cluster (ONC) appears to be unusual on two grounds: the observed constellation of the OB stars of the entire ONC and its Trapezium at its centre implies a time-scale problem given the age of the Trapezium, and an initial mass function (IMF) problem for the whole OB star population in the ONC. Given the estimated crossing time of the Trapezium, it ought to have totally dynamically decayed by now. Furthermore, by combining the lower limit of the ONC mass with a standard IMF it emerges that the ONC should have formed at least about 40 stars heavier than 5 M ⊙ while only 10 are observed. Using the N-body experiments we (i) confirm the expected instability of the Trapezium and (ii) show that beginning with a compact OB-star configuration of about 40 stars both the number of observed OB stars after 1 Myr within 1 pc radius and a compact trapezium configuration can be reproduced. These two empirical constraints thus support our estimate of 40 initial OB stars in the cluster. Interestingly, a more-evolved version of the ONC resembles the Upper Scorpius OB association. The N-body experiments are performed with the new C-code CATENA by integrating the equations of motion using the chain-multiple-regularization method. In addition, we present a new numerical formulation of the IMF.
Torelli groups, extended Johnson homomorphisms, and new cycles on the moduli space of curves

Abstract Infinite presentations are given for all of the higher Torelli groups of once-punctured surfaces. In the case of the classical Torelli group, a finite presentation of the corresponding groupoid is also given, and finite presentations of the classical Torelli groups acting trivially on homology modulo N are derived for all N. Furthermore, the first Johnson homomorphism, which is defined from the classical Torelli group to the third exterior power of the homology of the surface, is shown to lift to an explicit canonical 1-cocycle of the Teichmüller space. The main tool for these results is the known mapping class group invariant ideal cell decomposition of the Teichmüller space. This new 1-cocycle is mapping class group equivariant, so various contractions of its powers yield various combinatorial (co)cycles of the moduli space of curves, which are also new. Our combinatorial construction can be related to former works of Kawazumi and the first-named author with the consequence that the algebra generated by the cohomology classes represented by the new cocycles is precisely the tautological algebra of the moduli space. There is finally a discussion of prospects for similarly finding cocycle lifts of the higher Johnson homomorphisms.
Genetic and Functional Interactions between the Mitochondrial Outer Membrane Proteins Tom6 and Sam37

ABSTRACT The TOM complex is the general mitochondrial entry site for newly synthesized proteins. Precursors of β-barrel proteins initially follow this common pathway and are then relayed to the SAM/TOB complex, which mediates their integration into the outer membrane. Three proteins, Sam50 (Tob55), Sam35 (Tob38/Tom38), and Sam37 (Mas37), have been identified as the core constituents of the latter complex. Sam37 is essential for growth at elevated temperatures, but the function of the protein is currently unresolved. To identify interacting partners of Sam37 and thus shed light on its function, we screened for multicopy suppressors of sam37Δ. We identified the small subunit of the TOM complex, Tom6, as such a suppressor and found a tight genetic interaction between the two proteins. Overexpression of SAM37 suppresses the growth phenotype of tom6Δ, and cells lacking both genes are not viable. The ability of large amounts of Tom6 to suppress the sam37Δ phenotype can be linked to the capacity of Tom6 to stabilize Tom40, an essential β-barrel protein which is the central component of the TOM complex. Our results suggest that Sam37 is required for growth at higher temperatures, since it enhances the biogenesis of Tom40, and this requirement can be overruled by improved stability of newly synthesized Tom40 molecules.
The Case for Process Fairness in Learning: Feature Selection for Fair Decision Making

Machine learning methods are increasingly being used to inform, or sometimes even directly to make, important decisions about humans. A number of recent works have focussed on the fairness of the outcomes of such decisions, particularly on avoiding decisions that affect users of different sensitive groups ( e.g. , race, gender) disparately. In this paper, we propose to consider the fairness of the process of decision making. Process fairness can be measured by estimating the degree to which people consider various features to be fair to use when making an important legal decision. We examine the task of predicting whether or not a prisoner is likely to commit a crime again once released by analyzing the dataset considered by ProPublica relating to the COMPAS system. We introduce new measures of people’s discomfort with using various features, show how these measures can be estimated, and consider the effect of removing the uncomfortable features on prediction accuracy and on outcome fairness. Our empirical analysis suggests that process fairness may be achieved with little cost to outcome fairness, but that some loss of accuracy is unavoidable.