Miracle-dz/UniFAR-FTUs huggingface dataset:
A Method for Predicting Protein-Protein Interaction Types

Protein-protein interactions (PPIs) govern basic cellular processes through signal transduction and complex formation. The diversity of those processes gives rise to a remarkable diversity of interactions types, ranging from transient phosphorylation interactions to stable covalent bonding. Despite our increasing knowledge on PPIs in humans and other species, their types remain relatively unexplored and few annotations of types exist in public databases. Here, we propose the first method for systematic prediction of PPI type based solely on the techniques by which the interaction was detected. We show that different detection methods are better suited for detecting specific types. We apply our method to ten interaction types on a large scale human PPI dataset. We evaluate the performance of the method using both internal cross validation and external data sources. In cross validation, we obtain an area under receiver operating characteristic (ROC) curve ranging from 0.65 to 0.97 with an average of 0.84 across the predicted types. Comparing the predicted interaction types to external data sources, we obtained significant agreements for phosphorylation and ubiquitination interactions, with hypergeometric p-value = 2.3e−54 and 5.6e−28 respectively. We examine the biological relevance of our predictions using known signaling pathways and chart the abundance of interaction types in cell processes. Finally, we investigate the cross-relations between different interaction types within the network and characterize the discovered patterns, or motifs. We expect the resulting annotated network to facilitate the reconstruction of process-specific subnetworks and assist in predicting protein function or interaction.
How to Determine Output Schemas of XQuery Queries

The XQuery language is the standard query language for XML. The result of XQuery queries are typically XML documents in other formats. We introduce the term output schemas of an XQuery query, which represents those schemas, to which the resultant XML documents of the considered XQuery query conform to. Output schemas of XQuery queries can be used to automatically detect the XQuery query, which has been used for querying, of target XML documents or to reason on the output schema without access to the resultant XML documents for a static analysis of the used XQuery query. In this paper, we describe the automatic determination of an output schema of a given XQuery query. The input of our proposed output schema generator is the used XQuery query and the schema of the input XML documents.
Pathogenicity of the highly leukotoxic JP2 clone of Aggregatibacter actinomycetemcomitans and its geographic dissemination and role in aggressive periodontitis

For decades, Aggregatibacter actinomycetemcomitans has been associated with aggressive forms of periodontitis in adolescents. In the middle of the 1990s, a specific JP2 clone of A. actinomycetemcomitans, belonging to the cluster of serotype b strains of A. actinomycetemcomitans and having a number of other characteristics, was found to be strongly associated with aggressive forms of periodontitis, particularly in North Africa. Although several longitudinal studies still point to the bacterial species, A. actinomycetemcomitans as a risk factor of aggressive periodontitis, it is now also widely accepted that the highly leukotoxic JP2 clone of A. actinomycetemcomitans is implicated in rapidly progressing forms of aggressive periodontitis. The JP2 clone strains are highly prevalent in human populations living in Northern and Western parts of Africa. These strains are also prevalent in geographically widespread populations that have originated from the Northwest Africa. Only sporadic signs of a dissemination of the JP2 clone strains to non-African populations have been found despite Africans living geographically widespread for hundreds of years. It remains an unanswered question if a particular host tropism exists as a possible explanation for the frequent colonization of the Northwest African population with the JP2 clone. Two exotoxins of A. actinomycetemcomitans are known, leukotoxin (LtxA) and cytolethal distending toxin (Cdt). LtxA is able to kill human immune cells, and Cdt can block cell cycle progression in eukaryotic cells and thus induce cell cycle arrest. Whereas the leukotoxin production is enhanced in JP2 clone strains thus increasing the virulence potential of A. actinomycetemcomitans, it has not been possible so far to demonstrate such a role for Cdt. Lines of evidence have led to the understanding of the highly leukotoxic JP2 clone of A. actinomycetemcomitans as an aetiological factor of aggressive periodontitis. Patients, who are colonized with the JP2 clone, are likely to share this clone with several family members because the clone is transmitted through close contacts. This is a challenge to the clinicians. The patients need intense monitoring of their periodontal status as the risk for developing severely progressing periodontal lesions are relatively high. Furthermore, timely periodontal treatment, in some cases including periodontal surgery supplemented by the use of antibiotics, is warranted. Preferably, periodontal attachment loss should be prevented by early detection of the JP2 clone of A. actinomycetemcomitans by microbial diagnostic testing and/or by preventive means.
Reduced cerebrospinal fluid 5‐hydroxyindoleacetic acid and homovanillic acid in children with epilepsy

Cerebrospinal fluid (CSF) concentrations of 5-hydroxyindoleacetic acid (5-HIAA), homovanillic acid (HVA) and probenecid were examined in 14 children with epilepsy (ages 6 months to 17 years) and 17 controls (ages 14 months to 16 years). The concentrations of amine metabolites were significantly correlated with probenecid concentrations in both groups of children. Cerebrospinal fluid concentrations of 5-HIAA were 63.6 ng per milliliter ± 8.23 S.E. M. and 117 ng per milliliter ± 11.6 S.E. M. for the epilepsy and control groups respectively. HVA averaged 89.1 ng per milliliter ± 15.2 S.E. M. in epilepsy and 172 ng per milliliter ± 19.2 S.E. M. in the control group. These findings indicate a significant difference between epilepsy and control groups. Probenecid concentrations were similar in each group. The reduced cerebrospinal fluid amine metabolite concentrations in children with epilepsy were not related to age, anticonvulsant medication, cerebrospinal fluid folate or protein concentration, or cerebrospinal fluid cell count. Our findings suggest a relationship between brain amines and epilepsy.
Specimens size, aggregate size, and aggregate type effect on spalling of concrete in fire

This paper attempted to isolate variables that govern concrete spalling when exposed to a hydrocarbon fire. The influence of specimen size was investigated by studying 4 specimen sizes consisting of cylinders, columns, and panels. Three aggregate sizes, 7 mm, 14 mm, and 20 mm were used in the concrete mixes to determine their effect on concrete spalling. Influence of aggregate type on concrete spalling was also investigated. Forty‐two different specimens were considered in this investigation. Concrete spalling was quantified as nominal spalling depth, which has been presented as a new way of quantifying the degree of concrete spalling. The results indicated that specimen size did have an effect on the spalling of concrete under hydrocarbon fire exposure and that nominal spalling depth of concrete increases as the specimen size increases. Aggregate size effect was evident when the maximum aggregate size increased from 7 mm to 20 mm, and explosive spalling was more severe for specimens with small size aggregates. Specimens with 14‐mm aggregate size showed inconsistent results and the spalling behavior witnessed was more random and sporadic. The type of aggregate used has no clear bearing on concrete spalling given both aggregates had similar linear expansion profiles.
Subchronic Effect of Silver Nanoparticles Following 28 Days of Repeated Oral Administration on Oxidative Stress, Inflammatory Biomarkers and DNA Fragmentation in Normal and Irradiated Rats

The present study was performed to evaluate the effect of 28 days subchronic oral administration of AgNPs in normal and irradiated rats (4 Gy). Oxidative stress biomarker (blood glutathione, serum nitric oxide and liver MDA as an index for lipid peroxidation), also some inflammatory parameters as c-reactive protein and tumor necrosis factor alpha (TNF-α) have been measured. Liver DNA fragmentation was examined to determine the damaging effect in liver tissues by gel electrophoresis technique. Results of the present study revealed that blood glutathione significantly increased in irradiated treated group irradiated with (4Gy) then treated with (42.599 mg/kg) (1/10 LD50 in irradiated animals) and in irradiated group (4Gy) as compared to normal control but the increase is more in the irradiated treated group. NO has been significantly increased in irradiated and irradiated treated group but with a lesser extent in irradiated treated group. All groups showed significant decrease in CRP as compared to normal control group. liverDNA fragmentation showed a damaging effect exhibited by AgNPs (26.878 mg/kg) (1/10 LD50 in normal animals) and irradiated treated group but to a lesser extent than AgNPs group, whereas vehicle Polyvinylpyrrolidone (PVP) and irradiation groups showed a damaging effects. Based on the present study we can conclude that AgNPs has a modulating effect in decreasing the elevated level of NO caused by irradiation. Meanwhile AgNPs potentiate the effect of irradiation on increasing blood glutathione level, decreases the damaging effect on liver DNA fragmentation caused by irradiation. These results can be promising in cancer patients receiving radiation therapy and treated with AgNPs, or those receiving AgNPs for any other medical purpose but such results awaits further investigations.
Effect of microbubble-induced capillary voids on the dispersion of sprays

The presence of bubbles and voids inside nozzles has a large effect on the morphology and atomization of sprays. In this investigation the voids formed by microbubbles entering the nozzle are investigated using transparent glass nozzles, pressure transducers, and high-speed diffuse backlight imaging. A correlation is found between the magnitude of pressure pulses inside the nozzle and the size of the bubbles causing these pulses. This relation allows the prediction of cavity formation also in nontransparent nozzles, which allow more realistic conditions of operation. Subsequently, the direct measurements of dispersion derived from the spread of glowing fluid showed no significant increase of the dispersion compared to cavitation-free conditions. This indicates that, while the spray angle may increase, the turbulence (in both liquid and gas phase) that governs the dispersion remains the same and the cavitation bubble events do not have a significant impact on this process.
What is keeping my phone awake?: characterizing and detecting no-sleep energy bugs in smartphone apps

Despite their immense popularity in recent years, smartphones are and will remain severely limited by their battery life. Preserving this critical resource has driven smartphone OSes to undergo a paradigm shift in power management: by default every component, including the CPU, stays off or in an idle state, unless the app explicitly instructs the OS to keep it on! Such a policy encumbers app developers to explicitly juggle power control APIs exported by the OS to keep the components on, during their active use by the app and off otherwise. The resulting power-encumbered programming unavoidably gives rise to a new class of software energy bugs on smartphones called no-sleep bugs, which arise from mis-handling power control APIs by apps or the framework and result in significant and unexpected battery drainage. This paper makes the first advances towards understanding and automatically detecting software energy bugs on smartphones. It makes the following three contributions: (1) we present the first comprehensive study of real world no-sleep energy bug characteristics; (2) we propose the first automatic solution to detect these bugs based on the classic reaching definitions dataflow analysis algorithm; (3) we provide experimental data showing that our tool accurately detected all 17 known instances of no-sleep bugs and found 34 new bugs in the 73 apps examined.
Mortality in Vermont granite workers and its association with silica exposure

Objectives To assess mortality in Vermont granite workers and examine relationships between silica exposure and mortality from lung cancer, kidney cancer, non-malignant kidney disease, silicosis and other non-malignant respiratory disease. Methods Workers employed between 1947 and 1998 were identified. Exposures were estimated using a job–exposure matrix. Mortality was assessed through 2004 and standardised mortality ratios (SMRs) were computed. Associations between mortality and exposure to silica were assessed by nested case–control analyses using conditional logistic regression. Results 7052 workers had sufficient data for statistical analysis. SMRs were significantly elevated for lung cancer (SMR 1.37, 95% CI 1.23 to 1.52), silicosis (SMR 59.13, 95% CI 44.55 to 76.97), tuberculosis (SMR 21.74, 95% CI 18.37 to 25.56) and other non-malignant respiratory disease (SMR 1.74, 95% CI 1.50 to 2.02) but not for kidney cancer or non-malignant kidney disease. In nested case–control analyses, significant associations with cumulative exposure to respirable free silica were observed for silicosis (OR 1.13, 95% CI 1.05 to 1.21 for each 1 mg/m3-year increase in cumulative exposure) and other non-malignant respiratory disease (OR 1.10, 95% CI 1.03 to 1.16) but not for lung cancer (OR 0.99, 95% CI 0.94 to 1.03), kidney cancer (OR 0.96, 95% CI 0.84 to 1.09) or non-malignant kidney disease (OR 0.95, 95% CI 0.84 to 1.08). Conclusions Exposure to crystalline silica in Vermont granite workers was associated with increased mortality from silicosis and other non-malignant respiratory disease, but there was no evidence that increased lung cancer mortality in the cohort was due to exposure. Mortality from malignant and non-malignant kidney disease was not significantly increased or associated with exposure.
Labor Market Experience and Worker Flows ∗ Aspen Gorry

This paper presents a model of learning where labor market experience improves the accuracy of information about the quality of future job matches. The model can explain the decline in both job finding and separation rates with age found in the data. Beyond accounting for labor market flows, the model gives predictions that are consistent with observed empirical wage distributions. I evaluate the effects of minimum wages on labor outcomes and find that the endogenous decline in job finding rates is essential to understand high unemployment rates for young workers subjected to minimum wages. Finally, I examine the lasting consequences for workers who start their careers in a bad economy. The model generates sizable wage losses that last eight to ten years without lasting differences in unemployment. These findings are consistent with empirical studies. ∗This is a copy of my job market paper. Please send comments to aspen@uchicago.edu. I thank my advisors Robert Shimer, Fernando Alvarez, Derek Neal, and Nancy Stokey for helpful comments. All mistakes are my own.
Burkholderia dabaoshanensis sp. nov., a Heavy-Metal-Tolerant Bacteria Isolated from Dabaoshan Mining Area Soil in China

Heavy-metal-tolerant bacteria, GIMN1.004T, was isolated from mine soils of Dabaoshan in South China, which were acidic (pH 2–4) and polluted with heavy metals. The isolation was Gram-negative, aerobic, non-spore-forming, and rod-shaped bacteria having a cellular width of 0.5−0.6 µm and a length of 1.3−1.8 µm. They showed a normal growth pattern at pH 4.0–9.0 in a temperature ranging from 5°C to 40°C.The organism contained ubiquinone Q-8 as the predominant isoprenoid quinine, and C16∶0, summed feature 8 (C18∶1 ω7c and C18∶1 ω6c), C18∶0, summed feature 3 (C16∶1 ω7c or iso-C15∶0 2-OH), C17∶0 cyclo, C18∶1 ω9c, C19∶0 cyclo ω8c, C14∶0 as major fatty acid. These profiles were similar to those reported for Burkholderia species. The DNA G+C % of this strain was 61.6%. Based on the similarity to 16S rRNA gene sequence, GIMN1.004T was considered to be in the genus Burkholderia. The similarities of 16S rRNA gene sequence between strain GIMN1.004T and members of the genus Burkholderia were 96−99.4%, indicating that this novel strain was phylogenetically related to members of that genus. The novel strain showed the highest sequence similarities to Burkholderia soli DSM 18235T (99.4%); Levels of DNA-DNA hybridization with DSM 18235T was 25%. Physiological and biochemical tests including cell wall composition analysis, differentiated phenotype of this strain from that closely related Burkholderia species. The isolation had great tolerance to cadmium with MIC of 22 mmol/L, and adsorbability of 144.94 mg/g cadmium,and it was found to exhibit antibiotic resistance characteristics. The adsorptive mechanism of GIMN1.004T for cadmium depended on the action of the amide,carboxy and phosphate of cell surface and producing low-molecular-weight (LMW ) organic acids to complex or chelated Cd2+. Therefore, the strain GIMN1.004T represented a new cadmium resistance species, which was tentatively named as Burkholderia dabaoshanensis sp. nov. The strain type is GIMN1.004T ( = CCTCC M 209109T = NRRL B-59553T ).
Cross-Layer Design of Optimal Contention Period for Mobile WiMAX Systems

In IEEE 802.16e mobile WiMAX system, since mobile stations (MSs) send bandwidth request (BR) messages to base station (BS) during contention period when they need uplink channel to transmit data in the case of multicast polling or broadcast polling, the uplink performance is affected by the size of the contention period in the uplink subframe. The access delay will be increased if the size of the contention period is too small and the resource will be wasted on the contrary. Therefore, we propose a cross-layer analytical model for designing the optimal size of the contention period. The model is simulated using OPNET modeler, and the results show that our proposed model can improve the uplink data transmission efficiency.
Connected component based technique for automatic ear detection

This paper presents an efficient technique for automatic ear detection from side face images. The proposed technique detects ear by exploiting its inherent structural details and is rotation, scale and shape invariant. It can detect ear without any training or assuming prior knowledge of the input image. The technique is based on connected component analysis of a graph constructed using the edge map of the image and is evaluated on a data set consisting of 2361 side face images collected at IIT Kanpur. Ear detection results are found to be very good and speak for the efficiency and robustness of the technique. To show the accuracy of the detection, detected ears are used for recognition and results are compared with the same obtained when ear cropping in done manually.
Oligocene and early miocene ruminants (mammalia, artiodactyla) from Pakistan and Uganda

Late Oligocene and Early Miocene fossil ruminants from Napak and Moroto in Uganda and the Zinda Pir sequence in Pakistan comprise at least eight taxa, including an indeterminate lophiomerycid, ? Gelocus gajensis, Walangania africanus, Bugtimeryx pilgrimi, an indeterminate large cervoid, Progiraffa exigua, Palaeohypsodontus zinensis, and an unnamed bovid. The fossils range in age between 25 and 16 million years old and together with species of tragulids provide evidence for the existence of diverse latest Oligocene and earliest Miocene ruminant faunas in sub-Saharan Africa and southern Asia. The fossils from Pakistan may also document the first appearance and subsequent radiation of giraffes and bovids, two groups that dominate later Neogene and modern herbivore faunas. John C. Barry. Peabody Museum and Department of Anthropology, Harvard University, 11 Divinity Ave., Cambridge, Massachusetts 02138 USA jcbarry@fas.harvard. edu Susanne Cote. Department of Anthropology, Harvard University, 11 Divinity Ave., Cambridge, Massachusetts 02138 USA Laura MacLatchy. Department of Anthopology, University of Michigan, 550 East University Ave., Ann Arbor, MI 48109-1092 USA Everett H. Lindsay. Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA Robert Kityo. Zoology Department, Makerere University, Kampala, Uganda A. Rahim Rajpar. Pakistan Museum of Natural History, Islamabad, Pakistan
Matrix metalloproteinases in vascular physiology and disease

Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that primarily degrade components of the extracellular matrix (ECM). Remodeling of the ECM by MMPs is important in both physiological and pathological processes, including organ generation/regeneration, angiogenesis, wound healing, inflammation and tumor growth. In the vasculature, MMPs play a role in beneficial processes such as angiogenesis, collateral artery formation and thrombus resolution. However, MMP expression is also implicated in the pathogenesis of vascular diseases such as atherosclerosis, aortic aneurysms, plaque rupture and neointimal hyperplasia after balloon angioplasty. Here, we review the structure, functions and roles of MMPs in both neovascularization and vascular pathology and discuss the potential of, and challenges that face, adapting MMPs as therapeutic targets in vascular disease.
Influence of different glass fiber reinforcements on denture base polymer strenght (Fiber reinforcements of dental polymer)

Aim: Assessment of flexural strength values of dental base polymers reinforced with different glass fibers ("dental" and "industrial" origin) after performed artificial ageing procedures. Methods: Three hundred specimens (dimensions 18 x 10 x 3 mm) were produced of denture base polymers reinforced with different glass fibers. The "short beam" testing method was used to determine the flexural strenght of the specimens after polymerization, immersion in water temperature 37C for 28 days, and thermo-cycling. Results: Flexural strength of the polymer specimens reinforced with glass fibers demonstrated rise of flexural strength values (103.10 - 163.88 MPa), no matter which type ("dental" or "industrial") fibers was used. Microscopic examination revealed partial bonding between the glass fibers and the polymer material. Conclusion: Both of the investigated glass fibers had similar strengthening effect, but due to the better investment/benefit ratio "industrial" glass fibers could be recommended for dental laboratory use. Prolonged polymerization of denture base materials should be proposed because it had direct impact on the improvement of flexural strength values.