Miracle-dz/UniFAR-FTUs huggingface dataset:
Holistic and scalable ranking of RDF data

The volume and number of data sources published using Semantic Web standards such as RDF grows continuously. The largest of these data sources now contain billions of facts and are updated periodically. A large number of applications driven by such data sources requires the ranking of entities and facts contained in such knowledge graphs. Hence, there is a need for time-efficient approaches that can compute ranks for entities and facts simultaneously. In this paper, we present the first holistic ranking approach for RDF data. Our approach, dubbed HARE, allows the simultaneous computation of ranks for RDF triples, resources, properties and literals. To this end, HARE relies on the representation of RDF graphs as bi-partite graphs. It then employs a time-efficient extension of the random walk paradigm to bi-partite graphs. We show that by virtue of this extension, the worst-case complexity of HARE is O(n5) while that of PageRank is O(n6). In addition, we evaluate the practical efficiency of our approach by comparing it with PageRank on 6 real and 6 synthetic datasets with sizes up to 108 triples. Our results show that HARE is up to 2 orders of magnitude faster than PageRank. We also present a brief evaluation of HARE's ranking accuracy by comparing it with that of PageRank applied directly to RDF graphs. Our evaluation on 19 classes of DBpedia demonstrates that there is no statistical difference between HARE and PageRank. We hence conclude that our approach goes beyond the state of the art by allowing the ranking of all RDF entities and of RDF triples without being worse w.r. t. the ranking quality it achieves on resources. HARE is open-source and is available at http://github.com/dice-group/hare.
Induction of Broad-Spectrum Protective Immunity against Disparate Cryptococcus Serotypes

Cryptococcosis is a fungal disease caused by multiple Cryptococcus serotypes; particularly C. neoformans (serotypes A and D) and C. gattii (serotypes B and C). To date, there is no clinically available vaccine to prevent cryptococcosis. Mice given an experimental pulmonary vaccination with a C. neoformans serotype A strain engineered to produce interferon-γ, denoted H99γ, are protected against a subsequent otherwise lethal experimental infection with C. neoformans serotype A. Thus, we determined the efficacy of immunization with C. neoformans strain H99γ to elicit broad-spectrum protection in BALB/c mice against multiple disparate Cryptococcus serotypes. We observed significantly increased survival rates and significantly decreased pulmonary fungal burden in H99γ immunized mice challenged with Cryptococcus serotypes A, B, or D compared to heat-killed H99γ (HKH99γ) immunized mice. Results indicated that prolonged protection against Cryptococcus serotypes B or D in H99γ immunized mice was CD4+ T cell dependent and associated with the induction of predominantly Th1-type cytokine responses. Interestingly, immunization with H99γ did not elicit greater protection against challenge with the Cryptococcus serotype C tested either due to low overall virulence of this strain or enhanced capacity of this strain to evade host immunity. Altogether, these studies provide “proof-of-concept” for the development of a cryptococcal vaccine that provides cross-protection against multiple disparate serotypes of Cryptococcus.
PNPLA 3 I 148 M Variant Influences Circulating Retinol in Adults with Nonalcoholic Fatty Liver Disease or Obesity 1 , 2

Background: Retinol is a lipid-soluble essential nutrient that is stored as retinyl esters in lipid droplets of hepatic stellate cells. Patatin-like phospholipase domain-containing 3 (PNPLA3), through its retinyl-palmitate lipase activity, releases retinol from lipid droplets in hepatic stellate cells in vitro and ex vivo. We have shown that the genetic variant I148M (rs738409) reduces the PNPLA3 retinyl-palmitate lipase activity. Objective: The aim of the present genetic association study was to test whether overweight/obese carriers of the PNPLA3 148M mutant allele had lower circulating concentrations of retinol than individuals who are homozygous for the 148I allele. Methods: PNPLA3 I148M (rs738409) was genotyped by Taqman assay in 76 overweight/obese individuals [BMI (kg/m) $25; mean 6 SD age: 59.7 6 11.4 y; male gender: 70%] with a histologic diagnosis of nonalcoholic fatty liver disease (NAFLD; namely the Milan NAFLD cohort) and in 413 obese men (BMI $30; mean 6 SD age: 57.1 6 4.9 y) from the a-Tocopherol, b-Carotene Cancer Prevention (ATBC) Study. Serum concentrations of retinol and a-tocopherol were measured by HPLC in both cohorts. b-Carotene concentrations in the ATBC study were measured by using HPLC. Results: The PNPLA3 148M mutant allele was associated with lower fasting circulating concentrations of retinol (b = 20.289, P = 0.03) in adults with NAFLD (Milan NAFLD cohort). The PNPLA3 148Mmutant allele was also associated with lower fasting circulating concentrations of retinol in adults with a BMI $30 (ATBC study; b = 20.043, P = 0.04). Conclusion:We showed for the first time, to our knowledge, that carriers of the PNPLA3 148M allele with either fatty liver plus obesity or obesity alone have lower fasting circulating retinol concentrations. J Nutr 2015;145:1687–91.
Private federated learning on vertically partitioned data via entity resolution and additively homomorphic encryption

Consider two data providers, each maintaining private records of different feature sets about common entities. They aim to learn a linear model jointly in a federated setting, namely, data is local and a shared model is trained from locally computed updates. In contrast with most work on distributed learning, in this scenario (i) data is split vertically, i.e. by features, (ii) only one data provider knows the target variable and (iii) entities are not linked across the data providers. Hence, to the challenge of private learning, we add the potentially negative consequences of mistakes in entity resolution. Our contribution is twofold. First, we describe a three-party end-to-end solution in two phases ---privacy-preserving entity resolution and federated logistic regression over messages encrypted with an additively homomorphic scheme---, secure against a honest-but-curious adversary. The system allows learning without either exposing data in the clear or sharing which entities the data providers have in common. Our implementation is as accurate as a naive non-private solution that brings all data in one place, and scales to problems with millions of entities with hundreds of features. Second, we provide what is to our knowledge the first formal analysis of the impact of entity resolution's mistakes on learning, with results on how optimal classifiers, empirical losses, margins and generalisation abilities are affected. Our results bring a clear and strong support for federated learning: under reasonable assumptions on the number and magnitude of entity resolution's mistakes, it can be extremely beneficial to carry out federated learning in the setting where each peer's data provides a significant uplift to the other.
Human Neutrophils Secrete Bioactive Paucimannosidic Proteins from Azurophilic Granules into Pathogen-Infected Sputum*

Background: Protein paucimannosylation is considered an important invertebrate- and plant-specific glycoepitope. Results: Azurophilic granule-specific human neutrophil proteins from pathogen-infected sputum displayed significant core-fucosylated paucimannosylation generated by maturation- and granule-specific β-hexosaminidase A and were preferentially secreted from non-lysosomal origins into sputum upon P. aeruginosa stimulation. Conclusion: Human neutrophils produce, store, and selectively secrete bioactive paucimannosidic proteins. Significance: This work will aid in understanding the function(s) of human paucimannosylation in glycoimmunology. Unlike plants and invertebrates, mammals reportedly lack proteins displaying asparagine (N)-linked paucimannosylation (mannose1–3fucose0–1N-acetylglucosamine2Asn). Enabled by technology advancements in system-wide biomolecular characterization, we document that protein paucimannosylation is a significant host-derived molecular signature of neutrophil-rich sputum from pathogen-infected human lungs and is negligible in pathogen-free sputum. Five types of paucimannosidic N-glycans were carried by compartment-specific and inflammation-associated proteins of the azurophilic granules of human neutrophils including myeloperoxidase (MPO), azurocidin, and neutrophil elastase. The timely expressed human azurophilic granule-resident β-hexosaminidase A displayed the capacity to generate paucimannosidic N-glycans by trimming hybrid/complex type N-glycan intermediates with relative broad substrate specificity. Paucimannosidic N-glycoepitopes showed significant co-localization with β-hexosaminidase A and the azurophilic marker MPO in human neutrophils using immunocytochemistry. Furthermore, promyelocyte stage-specific expression of genes coding for paucimannosidic proteins and biosynthetic enzymes indicated a novel spatio-temporal biosynthetic route in early neutrophil maturation. The absence of bacterial exoglycosidase activities and paucimannosidic N-glycans excluded exogenous origins of paucimannosylation. Paucimannosidic proteins from isolated and sputum neutrophils were preferentially secreted upon inoculation with virulent Pseudomonas aeruginosa. Finally, paucimannosidic proteins displayed affinities to mannose-binding lectin, suggesting immune-related functions of paucimannosylation in activated human neutrophils. In conclusion, we are the first to document that human neutrophils produce, store and, upon activation, selectively secrete bioactive paucimannosidic proteins into sputum of lungs undergoing pathogen-based inflammation.
Structural templates for modeling homodimers

Oligomeric proteins are more abundant in nature than monomeric proteins, and involved in all biological processes. In the absence of an experimental structure, their subunits can be modeled from their sequence like monomeric proteins, but reliable procedures to build the oligomeric assembly are scarce. Template‐based methods, which start from known protein structures, are commonly applied to model subunits. We present a method to model homodimers that relies on a structural alignment of the subunits, and test it on a set of 511 target structures recently released by the Protein Data Bank, taking as templates the earlier released structures of 3108 homodimeric proteins (H‐set), and 2691 monomeric proteins that form dimer‐like assemblies in crystals (M‐set). The structural alignment identifies a H‐set template for 97% of the targets, and in half of the cases, it yields a correct model of the dimer geometry and residue–residue contacts in the target. It also identifies a M‐set template for most of the targets, and some of the crystal dimers are very similar to the target homodimers. The procedure efficiently detects homology at low levels of sequence identities, and points to erroneous quaternary structures in the Protein Data Bank. The high coverage of the target set suggests that the content of the Protein Data Bank already approaches the structural diversity of protein assemblies in nature, and that template‐based methods should become the choice method for modeling oligomeric as well as monomeric proteins.
A possible change in doubling time of haemopoietic progenitor cells with stem cell development

We separated haemopoietic progenitors derived from marrow cells of 5‐fluorouracil (5‐FU)‐treated mice into three groups, based on the stages of stem cell development and studied doubling time, using a serum‐free clonal culture system. Stage I progenitors were those present in primary marrow cells from 5‐FU‐treated mice. Stages II and III progenitors were early and late progenies in culture of stage I progenitors, respectively. The morphological analysis of colonies derived from stage I, II and III progenitors demonstrated an association of progression of stages with loss of multipotentiality. The doubling time of haemopoietic progenitors was estimated by sequential analysis of colony formation and studies of growth fraction. The time required for haemopoietic progenitors to double shortened as their stage of development progressed. Alteration in one doubling time of haemopoietic progenitors at progressive stages of stem cell development was seen in cultures supported by various combinations of growth factors, including interleukin‐3 (IL‐3), IL‐11, and steel factor (SF). Cell‐cycle analysis suggested that reduction of the doubling time of haemopoietic progenitors is probably due to a decrease in the time spent in the G1 phase of the cell cycle. Our results suggest that in early haemopoiesis the doubling time of haemopoietic progenitors may change with stem cell development.
Human DNA Polymerase (cid:2) Promotes Replication through a Ring-Closed Minor-Groove Adduct That Adopts a syn Conformation in DNA

Acrolein, an (cid:1) , (cid:2) -unsaturated aldehyde, is generated in vivo as the end product of lipid peroxidation and from oxidation of polyamines. The reaction of acrolein with the N 2 group of guanine in DNA leads to the formation of a cyclic adduct, (cid:3) -hydroxy-1, N 2 -propano-2 (cid:1) -deoxyguanosine ( (cid:3) -HOPdG). Previously, we have shown that proﬁcient replication through the (cid:3) -HOPdG adduct can be mediated by the sequential action of human DNA polymerases (Pols) (cid:4) and (cid:5) , in which Pol (cid:4) incorporates either pyrimidine opposite (cid:3) -HOPdG, but Pol (cid:5) extends only from the cytosine. Since (cid:3) -HOPdG can adopt either a ring-closed cyclic form or a ring-opened form in DNA, to better understand the mechanisms that Pols (cid:4) and (cid:5) employ to promote replication through this lesion, we have examined the ability of these polymerases to replicate through the structural analogs of (cid:3) -HOPdG that are permanently either ring closed or ring opened. Our studies with these model adducts show that whereas the ring-opened form of (cid:3) -HOPdG is not inhibitory to synthesis by human Pols (cid:6) , (cid:4) , or (cid:5) , only Pol (cid:4) is able to incorporate nucleotides opposite the ring-closed form, which is known to adopt a syn conformation in DNA. From these studies, we infer that (i) Pols (cid:6) , (cid:4) , and (cid:5) have the ability to proﬁciently replicate through minor-groove DNA lesions that do not perturb the Watson-Crick hydrogen bonding of the template base with the incoming nucleotide, and (ii) Pol (cid:4) can accommodate a minor-groove-adducted template purine which adopts a syn conformation in DNA and forms a Hoogsteen base pair with the incoming nucleotide. DNA polymerases of the Y family promote replication through distorting DNA lesions. DNA polymerase (cid:3) (Pol (cid:3) is distinct from other members of this family by virtue of its ability to replicate through cyclobutane pyrimidine dimers, and Pol (cid:3) from both Saccharomyces cerevisiae and humans incorporates an A opposite the 3 (cid:4) T and the 5 (cid:4) T of a cis-syn TT dimer with the same efﬁciency and ﬁdelity as it does the corresponding undamaged T’s 8, 22, 25). Pol derives an open active site that both nucleotides the cyclobutane
Real-Time Public Transport Navigation on Smartwatches: A Comparison with a Smartphone-based Solution

In a rapidly growing mobile device market, a new and unique type of IT product, the smartwatch, has started gaining the users' attention. After several years of technological development, it has finally become a viable device that extends the functions of a smartphone to a more intimate level. In the industry of smart devices, particularly in wearable devices, smartwatches are widely considered as the next big thing which is going to have a significant impact on our daily lives. However, smartwatches still have a limited use in public transport information systems. In this paper, we present promising use cases for smartwatches in public transport which were extracted through a survey questionnaire we conducted. We designed and developed a prototype to realize one of the most promising use cases: real-time public transport navigation. We evaluated our prototype in a comprehensive user study. The comparison of the smartwatch-based navigation with a pure smartphone-based solution shows that the smartwatch outperforms the smartphone in all user experience metrics.
Low-Power Widely Tunable Gm-C Filter Employing an Adaptive DC-blocking, Triode-Biased MOSFET Transconductor

We propose a transconductor capable of providing a wide continuous-tuning-range filter applicable to Bluetooth, W-CDMA, LTE, and IEEE 802.11a/b/g W-LANs without sacrificing power consumption or die area. The wide tuning range is achieved without the need for any array configuration, using triode-biased input MOSFETs with transconductance that is widely tunable by means of drain bias adjustment. The transconductor also uses an adaptive DC-blocking circuit that suppresses bias current in a high transconductance mode, which results in minimizing transconductor power consumption.A 4th-order Butterworth low-pass filter using this transconductor, fabricated in a 0.18-μm CMOS process, exhibits a cut-off frequency tuning range of 0.3-12 MHz with a current consumption of 0.6-2.6 mA. The die area is small: 0.125 mm2.
Randomized Trial Influence of CYP 2 D 6 Activity on Pre-emptive Analgesia by the N-Methyl-D-Aspartate Antagonist Dextromethorphan in a Randomized Controlled Trial of Acute Pain

There is some evidence that dextromethorphan (DM) is effective as a preemptive analgesic agent. DM is mainly metabolized to dextrorphan (DOR) by CYP2D6 whose activity can be inhibited by pharmacologic intervention. EHRET, Georg Benedikt, et al. Influence of CYP2D6 activity on pre-emptive analgesia by the N-methyl-D-aspartate antagonist dextromethorphan in a randomized controlled trial of acute pain. Pain Physician, 2013, vol. 16, no. 1, p. 45-56
Comparison Between Veress Needle ( Closed ) Technique and Open Technique in Laparoscopic Cholecystectomy

Background: The aim of this study is to compare open cholecystectomy with needle (closed) technique in laparoscopic cholecystectomy in terms of outcomes and complications. Methods : In this comparative study patients undergoing cholecystectomy were randomized to be in either of the two groups. Each containing 70 patients. Inclusion criteria was, patients with age 20 to 50 years with symptomatic gall stones disease, and without any other general contraindication for laparoscopic surgery . All patients were diagnosed by history ultrasound abdomen. All patients having contraindications to laparoscopic procedure like respiratory compromise, malignancy or any other comorbidities were excluded from the study.Group A constituted 70 patients and all those were randomized for open technique while group B also contained the same number of patients and they were randomized for Veress needle technique. Open technique was performed through skin incision and then dissecting the fascia for gaining access to abdomen by inserting trocar while the closed technique involves direct insertion of Veress needle into abdominal cavity for pneumoperitoneum creation and then trocar placement. The parameters compared were access time , gas leak, visceral injury, vascular injury, need for conversion, umbilical port site hematoma, umbilical port site infection, umbilical port site hernia. Patients were assessed after discharge at the first post operative day, seventh day then after 2 months, 6 months, and after 1 year and last visit on 18 months for assessment of
Subjective Numeracy Scale as a Tool for Assessing Statistical Numeracy in Older Adult Populations

Background: Statistical numeracy, necessary for making informed medical decisions, is reduced among older adults who make more decisions about their medical care and treatment than at any other stage of life. Objective numeracy scales are a source of anxiety among patients, heightened among older adults. Objective: We investigate the subjective numeracy scale as an alternative tool for measuring statistical numeracy with older adult samples. Methods: Numeracy was assessed using objective measures for 526 adults ranging in age from 18 to 93 years, and all participants provided subjective numeracy ratings. Results: Subjective numeracy correlated highly with objective measurements among oldest adults (70+ years; r = 0.51, 95% CI 0.32, 0.66), and for younger age groups. Subjective numeracy explained 33.2% of age differences in objective numeracy. Conclusion: The subjective numeracy scale provides an effective tool for assessing statistical numeracy for broad age ranges and circumvents problems associated with objective numeracy measures.
Supporting pre-service teachers in designing technology-infused lesson plans

The present study compared the effectiveness of two types of just-in-time support for lesson planning. Both types contained the same technological information but differed regarding pedagogical and content information. The first type presented this information separately i.e., separate support; the second type presented this information in an integrated way i.e., integrated support. In an experimental design pre-service biology teachers received either the integrated support n=26 or separate support n=27. They were instructed to create a technology-infused lesson plan and justify their design decisions. Results showed that pre-service teachers who used the integrated support had more integrated pedagogical and content-related justifications and higher quality lesson plans than the group who received separate support. Both groups had few technology-related justifications, and technology integration was of low quality. These findings confirm the alleged superiority of integrated support over separate support, and suggest that additional guidance is needed for pre-service teachers to fully integrate technological, pedagogical and content information during lesson planning.
Effects of exercise at different times on postprandial lipemia and endothelial function.

PURPOSE The purpose of this study was to examine the effects of previous exercise on metabolic, hormonal, and endothelial responses to an oral fat-tolerance test (OFTT). METHODS Twelve healthy, recreationally trained men (age = 22.3 +/- 2.5 yr, weight = 80.7 +/- 12.4 kg, BMI = 25.1 +/- 3.1 kg.m(-2)) volunteered for this study. In a crossover fashion, subjects completed three OFTT trials that involved no exercise (NoEx) or exercise performed 16 h (EX-16) or 4 h (EX-4) before the ingestion of a meal (13 kcal.kg(-1) and 1.4 g of fat per kilogram of body weight). Blood was collected before and after the meal and hourly for 6 h. Brachial artery reactivity was measured using ultrasound before and at 2, 4, and 6 h after the meal. Dietary intake and exercise were standardized 4 d before the OFTT. The exercise session consisted of six resistance exercises and 30 min of running on a treadmill. The washout period between trials was, on average, 5 d. RESULTS Compared with NoEx, there were significant (P < 0.05) decreases in triglyceride area under the curve (AUC) during EX-16 (-26%) and EX-4 (-15%). Compared with NoEx, there were decreases in insulin AUC during EX-16 (-7%, P < 0.05) and EX-4 (-5%, NS). EX-4 resulted in a significantly larger fasting arterial diameter than EX-16 and NoEx, but there were no other significant effects on endothelial function. Lipemic variables did not show correlations with endothelium function for any of the trials. CONCLUSION An acute exercise session, regardless of the time point chosen (i.e., EX-16 or EX-4), reduced to a similar extent the total and incremental lipemic responses compared with the NoEx condition.