Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple-Drug Resistant Shiga Toxin-Producing E. coli in Raw Milk of Dairy Bovine

Introduction: Raw milk may contain pathogenic microorganisms harmful to humans, e.g., multidrug-resistant Escherichia coli non-O157:H7, which can cause severe colitis, hemolytic uremia, and meningitis in children. No studies are available on the prevalence of Shiga toxin-producing E. coli (STEC O157:H7) in sick or healthy dairy animals in the Khyber Pakhtunkhwa Province of Pakistan. Aim: This study aimed to isolate, characterize, and detect antibiotic resistance in STEC non-O157:H7 from unpasteurized milk of dairy bovines in this province. Materials and Methods: We collected raw milk samples (n = 800) from dairy farms, street vendors, and milk shops from different parts of the Khyber Pakhtunkhwa Province. E. coli was isolated from these samples followed by latex agglutination tests for serotyping. The detection of STEC was conducted phenotypically and confirmed by the detection of virulence genes genotypically. An antibiogram of STEC isolates was performed against 12 antibiotics using the disc diffusion method. Results: A total of 321 (40.12%) samples were found to be positive for E. coli in this study. These samples were processed for the presence of four virulence genes (Stx1, Stx2, ehxA, eae). Forty samples (5.0%) were STEC-positive. Of these, 38%, 25%, 19%, and 18% were positive for Stx1, Stx2, ehxA, and eae, respectively. Genotypically, we found that 1.37% of STEC isolates produced extended-spectrum beta-lactamase (ESBL) and contained the blaCTX M gene. Resistance to various antibiotics ranged from 18% to 77%. Conclusion: This study highlights the risk of virulent and multidrug-resistant STEC non-O157:H7 in raw milk and the need for proper quality surveillance and assurance plans to mitigate the potential public health threat.
Detection of adenovirus‐specific T cells in children with adenovirus infection after allogeneic stem cell transplantation

Human adenovirus (ADV) infection is an important complication post allogeneic stem cell transplantation (SCT), especially in children, with significant morbidity and mortality despite new antiviral treatment strategies. Although the control of infection seems to require T cells, characterization of ADV‐specific T cells post‐SCT has not been reported to date. Therefore, we prospectively studied the occurrence of ADV‐specific T cells in children with (n = 21) and without (n = 25) ADV‐infection postallogeneic SCT and in healthy donors (n = 53). ADV‐associated mortality occurred in seven of 21 children. After stimulation ex vivo with ADV‐lysate, interferon‐γ‐secreting T cells were analysed by flow cytometry. All the patients with ADV‐associated mortality had no specific T cells, although reconstitution of absolute lymphocyte counts exceeded 0·3 × 109/l within 30 d post‐transplant. Patients who cleared ADV infection had significantly higher frequencies (mean ± standard deviation, 0·56 ± 0·5%) of ADV‐specific T cells until day 200 post‐SCT, than patients without ADV‐infection (0·12 ± 0·1%). These data suggest that ADV‐specific T‐cell reconstitution is protective against life‐threatening ADV‐infections postallogeneic SCT.
A dynamical analysis of the 14 Herculis planetary system

Precision radial velocity (RV) measurements of the Sun-like dwarf 14 Herculis published by Naef et. al (2004), Butler et. al (2006) and Wittenmyer et al (2007) reveal a Jovian planet in a 1760 day orbit and a trend indicating the second distant object. On the grounds of dynamical considerations, we test a hypothesis that the trend can be explained by the presence of an additional giant planet. We derive dynamical limits to the orbital parameters of the putative outer Jovian companion in an orbit within ∼ 13 AU. In this case, the mutual interactions between the Jovian planets are important for the long-term stability of the system. The best self-consistent and stable Newtonian fit to an edge-on config uration of Jovian planets has the outer planet in 9 AU orbit with a moderate eccentricity ∼ 0.2 and confined to a zone spanned by the low-order mean motion resonances 5:1 and 6:1. This solution lies in a shallow minimum of (χ 2) 1/2 and persists over a wide range of the system inclination. Other stable configurations within 1 σ confidence interval of the best fit are possible for the semi-m ajor axis of the outer planet in the range of (6,13) AU and the eccentricity in the range of (0,0.3). The orbital inclination cannot yet be determined but when it decreases, both planetary masses approach ∼ 10mJ and for i ∼ 30 o the hierarchy of the masses is reversed.
Predicting Drug-Target Interactions via Within-Score and Between-Score

Network inference and local classification models have been shown to be useful in predicting newly potential drug-target interactions (DTIs) for assisting in drug discovery or drug repositioning. The idea is to represent drugs, targets, and their interactions as a bipartite network or an adjacent matrix. However, existing methods have not yet addressed appropriately several issues, such as the powerless inference in the case of isolated subnetworks, the biased classifiers derived from insufficient positive samples, the need of training a number of local classifiers, and the unavailable relationship between known DTIs and unapproved drug-target pairs (DTPs). Designing more effective approaches to address those issues is always desirable. In this paper, after presenting better drug similarities and target similarities, we characterize each DTP as a feature vector of within-scores and between-scores so as to hold the following superiorities: (1) a uniform vector of all types of DTPs, (2) only one global classifier with less bias benefiting from adequate positive samples, and (3) more importantly, the visualized relationship between known DTIs and unapproved DTPs. The effectiveness of our approach is finally demonstrated via comparing with other popular methods under cross validation and predicting potential interactions for DTPs under the validation in existing databases.
The treatment of lymphedema.

BACKGROUND Before the treatment of arm lymphedema after breast carcinoma treatment with complex decongestive physiotherapy can be initiated, it is mandatory to differentiate between benign and malignant forms (due to relapse) and to establish the diagnosis of accompanying diseases, if present. METHODS In benign lymphedemas, the aim of complex decongestive physiotherapy is to restore the symptom free "Stage 0 of latency" and to maintain fitness for work. The palliative treatment of malignant lymphedemas results in the amelioration of the quality of life. RESULTS The results of treatment depend on the experience of the physician in clinical lymphology, on the training and dedication of the lymphedema therapist, and on the compliance of the patient. CONCLUSIONS A study concerning gene expression has shown that complex decongestive physiotherapy influences the pathological alterations of the interstitium in lymphedema patients.
C2-bound: a capacity and concurrency driven analytical model for many-core design

In this paper, we propose C2-Bound, a data-driven analytical model, that incorporates both memory capacity and data access concurrency factors to optimize many-core design. C2-Bound is characterized by combining the newly proposed latency model, concurrent average memory access time (C-AMAT), with the well-known memory-bounded speedup model (Sun-Ni's law) to facilitate computing tasks. Compared to traditional chip designs that lack the notion of memory concurrency and memory capacity, C2-Bound model finds memory bound factors significantly impact the optimal number of cores as well as their optimal silicon area allocations, especially for data-intensive applications with a none parallelizable sequential portion. Therefore, our model is valuable to the design of new generation many-core architectures that target big data processing, where working sets are usually larger than conventional scientific computing. These findings are evidenced by our detailed simulations, which show with C2-Bound the design space can be narrowed down significantly up to four orders of magnitude. C2-Bound analytic results can be either used in reconfigurable hardware environments or, by software designers, applied to scheduling, partitioning, and allocating resources among diverse applications.
Sex-specific ecophysiological responses to environmental fluctuations of free-ranging Hermann's tortoises: implication for conservation

We assessed the range of variation of physiological indicators (e.g. glucocorticoid) and movements in the endangered Hermann's tortoises. The findings provide sex-specific seasonal baselines that can be used to monitor the health status of tortoises facing environmental threats or during conservation actions (e.g. translocation).
Global diversification of a tropical plant growth form: environmental correlates and historical contingencies in climbing palms

Tropical rain forests (TRF) are the most diverse terrestrial biome on Earth, but the diversification dynamics of their constituent growth forms remain largely unexplored. Climbing plants contribute significantly to species diversity and ecosystem processes in TRF. We investigate the broad-scale patterns and drivers of species richness as well as the diversification history of climbing and non-climbing palms (Arecaceae). We quantify to what extent macroecological diversity patterns are related to contemporary climate, forest canopy height, and paleoclimatic changes. We test whether diversification rates are higher for climbing than non-climbing palms and estimate the origin of the climbing habit. Climbers account for 22% of global palm species diversity, mostly concentrated in Southeast Asia. Global variation in climbing palm species richness can be partly explained by past and present-day climate and rain forest canopy height, but regional differences in residual species richness after accounting for current and past differences in environment suggest a strong role of historical contingencies in climbing palm diversification. Climbing palms show a higher net diversification rate than non-climbers. Diversification analyses of palms detected a diversification rate increase along the branches leading to the most species-rich clade of climbers. Ancestral character reconstructions revealed that the climbing habit originated between early Eocene and Miocene. These results imply that changes from non-climbing to climbing habits may have played an important role in palm diversification, resulting in the origin of one fifth of all palm species. We suggest that, in addition to current climate and paleoclimatic changes after the late Neogene, present-day diversity of climbing palms can be explained by morpho-anatomical innovations, the biogeographic history of Southeast Asia, and/or ecological opportunities due to the diversification of high-stature dipterocarps in Asian TRFs.
Long noncoding RNA in liver diseases

The identification of the presence of large RNA transcripts that do not code for proteins but that may have biological functions has provided an important new perspective in gene regulation. These long noncoding RNAs (lncRNAs) are being increasingly recognized to contribute to many biological processes through diverse mechanisms. The roles of these emerging genes are being recognized across kingdoms. These findings are profoundly altering our understanding of disease pathobiology and leading to the emergence of new biological concepts underlying human diseases. Strategies for the discovery and characterization of lncRNAs are highlighted. Several lncRNAs have been described in liver disease, and in liver cancers in particular. Their molecular mechanisms of action, function, and contributions to disease pathophysiology are reviewed. LncRNA genes associated with liver diseases have potential roles as biomarkers of disease diagnosis, prognosis, or therapeutic response as well as direct targets for therapeutic intervention. Conclusion: The emerging knowledge in this rapidly advancing field offers promise for new fundamental knowledge and clinical applications that will be relevant for human liver diseases. (Hepatology 2014;60:744–753)
Protein complexes and functional modules in molecular networks

Proteins, nucleic acids, and small molecules form a dense network of molecular interactions in a cell. Molecules are nodes of this network, and the interactions between them are edges. The architecture of molecular networks can reveal important principles of cellular organization and function, similarly to the way that protein structure tells us about the function and organization of a protein. Computational analysis of molecular networks has been primarily concerned with node degree [Wagner, A. & Fell, D. A. (2001) Proc. R. Soc. London Ser. B 268, 1803–1810; Jeong, H. , Tombor, B. , Albert, R. , Oltvai, Z. N. & Barabasi, A. L. (2000) Nature 407, 651–654] or degree correlation [Maslov, S. & Sneppen, K. (2002) Science 296, 910–913], and hence focused on single/two-body properties of these networks. Here, by analyzing the multibody structure of the network of protein–protein interactions, we discovered molecular modules that are densely connected within themselves but sparsely connected with the rest of the network. Comparison with experimental data and functional annotation of genes showed two types of modules: (i) protein complexes (splicing machinery, transcription factors, etc.) and (ii) dynamic functional units (signaling cascades, cell-cycle regulation, etc.). Discovered modules are highly statistically significant, as is evident from comparison with random graphs, and are robust to noise in the data. Our results provide strong support for the network modularity principle introduced by Hartwell et al. [Hartwell, L. H. , Hopfield, J. J., Leibler, S. & Murray, A. W. (1999) Nature 402, C47–C52], suggesting that found modules constitute the “building blocks” of molecular networks.
Genetic Algorithm Based Parameter Identification of Defocused Image

A method to identify the degradation parameter of the defocused blur image based on genetic algorithm is proposed. In this technique, a FFT transform is performed in the frequency domain to estimate the range of defocus parameter, and then genetic algorithm is used to search in this domain to find the accurate value of the radius. We experimentally illustrate its performance; results show that the proposed parameter estimation technique is closely to the real defocus radius and more robust to noise.
Mechanical Characteristics of Individualized Biodegradable Augmentation Scaffold—In Vitro Pilot Study

The alveolar ridge reconstruction of vertical and combined bone defects is a non-predictable procedure with varying percentages of success. The greatest challenge for vertical and combined bone augmentation is to maintain mechanical stability of the bone graft; therefore, it is mandatory to provide and preserve space for bone regeneration. The development of biomaterials and 3D printing has enabled the use of polymer scaffolds in the reconstruction of alveolar ridge defects. The aim of this pilot study was to evaluate the mechanical characteristics of an innovative individualized biodegradable polylactic acid (PLA) scaffold, under dynamic conditions, simulating biodegradation and the influence of masticatory forces. After the design and 3D printing of PLA scaffolds, two groups of 27 scaffolds were formed according to the compression testing procedure. The compression tests were performed in occlusal and lateral directions. In each of the two groups, nine subgroups of three scaffolds were formed for different testing periods during in vitro degradation with a total period of 16 weeks. Results showed that biodegradation and load application had no significant influence on mechanical characteristics of tested scaffolds. It can be concluded that simulated masticatory forces and biodegradation do not significantly influence the mechanical characteristics of an individualized biodegradable augmentation scaffold.
FUZZY EVIDENCE THEORETIC APPROACHES FOR KNOWLEDGE DISCOVERY IN SPATIAL UNCERTAINTY DATA SETS

Although uncertainties exist in spatial knowledge discovery, they have not been paid much attention to. In the past years, the most researches of spatial knowledge discovery focused on the methods of data mining and its algorithms. In this paper, uncertainty and its propagation of spatial data are discussed and analysed firstly. Then, uncertainties at various stages of spatial knowledge discovery are briefly analysed, including data selection, data preprocessing, data mining, knowledge representation and uncertain reasoning. Thirdly, a method of spatial knowledge discovery in conjunction with uncertain reasoning by means of fuzzy evidence theory is proposed. Herein, the framework for uncertainty handling in spatial knowledge discovery is constructed, and the fundamental issues include soft discretization of spatial data, fuzzy transformation between quantitative data and qualitative concept, reasoning under uncertainty and uncertain knowledge representation.
Mutations of the CHK2 gene are found in some osteosarcomas, but are rare in breast, lung, and ovarian tumors

Checkpoint genes, activated in response to DNA damage and other stresses, are frequently targeted for alteration in cancer. Checkpoint kinase 2 (CHK2, CDS1, RAD53) is activated by ataxia telangiectasia mutated (ATM) in response to γ irradiation. Activated CHK2 stabilizes TP53, and acts on other cell cycle and stress regulators. These findings place CHK2 in the middle of a pathway frequently targeted in cancer. Because of this, and the observation that CHK2 mutations are inherited in some Li‐Fraumeni cancer syndrome families, we decided to examine the role of CHK2 mutations in sporadic cancers. Exploiting the genomic sequence of chromosome 22, we looked for mutations in the exons and intron junctions of the CHK2 gene in DNA samples from 170 patients (57 osteosarcomas, 25 other sarcomas, 35 nonsmall‐cell lung, 20 ovarian, and 33 breast cancers). Missense mutations affecting the forkhead and kinase domains were detected in four osteosarcomas and in one ovarian and one lung cancer. These findings of CHK2 gene mutations are consistent with osteosarcoma being a defining tumor of Li‐Fraumeni syndrome. The occurrence of CHK2 mutations in sporadic cancers emphasizes the importance of the stress pathway which includes TP53.
On the Independent Domination Number of Random Regular Graphs

A dominating set $\cal D$ of a graph $G$ is a subset of $V(G)$ such that, for every vertex $v\in V(G)$, either in $v\in {\cal D}$ or there exists a vertex $u \in {\cal D}$ that is adjacent to $v$. We are interested in finding dominating sets of small cardinality. A dominating set $\cal I$ of a graph $G$ is said to be independent if no two vertices of ${\cal I}$ are connected by an edge of $G$. The size of a smallest independent dominating set of a graph $G$ is the independent domination number of $G$. In this paper we present upper bounds on the independent domination number of random regular graphs. This is achieved by analysing the performance of a randomized greedy algorithm on random regular graphs using differential equations.
Modeling environmental contamination in hospital single‐ and four‐bed rooms

Abstract Aerial dispersion of pathogens is recognized as a potential transmission route for hospital acquired infections; however, little is known about the link between healthcare worker (HCW) contacts’ with contaminated surfaces, the transmission of infections and hospital room design. We combine computational fluid dynamics (CFD) simulations of bioaerosol deposition with a validated probabilistic HCW–surface contact model to estimate the relative quantity of pathogens accrued on hands during six types of care procedures in two room types. Results demonstrate that care type is most influential (P < 0.001), followed by the number of surface contacts (P < 0.001) and the distribution of surface pathogens (P = 0.05). Highest hand contamination was predicted during Personal care despite the highest levels of hand hygiene. Ventilation rates of 6 ac/h vs. 4 ac/h showed only minor reductions in predicted hand colonization. Pathogens accrued on hands decreased monotonically after patient care in single rooms due to the physical barrier of bioaerosol transmission between rooms and subsequent hand sanitation. Conversely, contamination was predicted to increase during contact with patients in four‐bed rooms due to spatial spread of pathogens. Location of the infectious patient with respect to ventilation played a key role in determining pathogen loadings (P = 0.05).
What is a good buffer cache replacement scheme for mobile flash storage?

Smartphones are becoming ubiquitous and powerful. The Achilles' heel in such devices that limits performance is the storage. Low-end flash memory is the storage technology of choice in such devices due to energy, size, and cost considerations. In this paper, we take a critical look at the performance of flash on smartphones for mobile applications. Specifically, we ask the question whether the state-of-the-art buffer cache replacement schemes proposed thus far (both flash-agnostic and flash-aware ones) are the right ones for mobile flash storage. To answer this question, we first expose the limitations of current buffer cache performance evaluation methods, and propose a novel evaluation framework that is a hybrid between trace-driven simulation and real implementation of such schemes inside an operating system. Such an evaluation reveals some unexpected and surprising insights on the performance of buffer management schemes that contradicts conventional wisdom. Armed with this knowledge, we propose a new buffer cache replacement scheme called SpatialClock. Using our evaluation framework, we show the superior performance of SpatialClock relative to the state-of-the-art for mobile flash storage.
Best practices in strategic information systems planning: a case study from the financial services industry

Increasing competitive pressures are requiring service based enterprises to change the way in whiclh they automate business processes, improve customer satisfaction, and match technology capabilities to business need. One of the major pressures being felt is the time sensitivity of information systems development. This study of senior IS professionals and business leaders in fu? teen financial institutions, focuses on the relationship between the time required to perform Strategic Information Systems Planning (SU3P) and the time required to satisfactorily implement these plans. Our preliminary conclusions are that systems development professionals will require more strategic business planning skills and structural thinking knowledge to be successfii in the future.
Sensitivity of c‐erbB Positive Cells to a Ligand Toxin and Its Utility in Purging Breast Cancer Cells from Peripheral Blood Stem Cell (PBSC) Collections

Autografting following high‐dose conditioning is being increasingly offered to breast cancer sufferers, without due regard to the reinfusion of malignant cells. We sought to determine if a breast cancer cell line could be successfully purged from peripheral blood stem cell (PBSC) harvests using a ligand‐toxin molecule directed to heregulin‐activated erbB receptors. Initial experiments demonstrated no reduction in hemopoietic colony‐forming ability in the presence of ligand toxin (2 nM). Breast cancer cell lines which demonstrated differing sensitivities to the ligand toxin were subsequently seeded into stem cell collections and incubated with 2 nM ligand‐toxin. One cell line, ZR‐75‐1, was completely sensitive to the ligand toxin in this mixture; a second, MDB‐MA‐361, was more profoundly sensitive to the ligand toxin in the presence of the PBSC, whereas a third was unaffected by the toxin. These results suggest purging may indeed be possible in the PBSC of breast cancer patients, but the parameters that define sensitivity are as yet unknown.