Miracle-dz/UniFAR-FTUs huggingface dataset:
Niches, Population Structure and Genome Reduction in Ochrobactrum intermedium: Clues to Technology-Driven Emergence of Pathogens

Ochrobactrum intermedium is considered as an emerging human environmental opportunistic pathogen with mild virulence. The distribution of isolates and sequences described in literature and databases showed frequent association with human beings and polluted environments. As population structures are related to bacterial lifestyles, we investigated by multi-locus approach the genetic structure of a population of 65 isolates representative of the known natural distribution of O. intermedium. The population was further surveyed for genome dynamics using pulsed-field gel electrophoresis and genomics. The population displayed a clonal epidemic structure with events of recombination that occurred mainly in clonal complexes. Concerning biogeography, clones were shared by human and environments and were both cosmopolitan and local. The main cosmopolitan clone was genetically and genomically stable, and grouped isolates that all harbored an atypical insertion in the rrs. Ubiquitism and stability of this major clone suggested a clonal succes in a particular niche. Events of genomic reduction were detected in the population and the deleted genomic content was described for one isolate. O. intermedium displayed allopatric characters associated to a tendancy of genome reduction suggesting a specialization process. Considering its relatedness with Brucella, this specialization might be a commitment toward pathogenic life-style that could be driven by technological selective pressure related medical and industrial technologies.
Developmental Cognitive Neuroscience Reduced Reward Anticipation in Youth at High-risk for Unipolar Depression: a Preliminary Study

Offspring of depressed parents are at risk for depression and recent evidence suggests that reduced positive affect (PA) may be a marker of risk. We investigated whether self-reports of PA and fMRI-measured striatal response to reward, a neural correlate of PA, are reduced in adolescent youth at high familial risk for depression (HR) relative to youth at low familial risk for depression (LR). Functional magnetic resonance imaging assessments were conducted with 14 HR and 12 LR youth. All youth completed an ecological momentary assessment protocol to measure PA in natural settings and a self-report measure of depression symptomatology. Analyses found that HR youth demonstrated lower striatal response than LR youth during both reward anticipation and outcome. However, after controlling for youth self-reports of depression, HR youth demonstrated lower striatal response than LR youth only during reward anticipation. No significant differences were found between HR and LR youth on subjective ratings of PA or depressive symptoms. Results are consistent with previous findings that reduced reward response is a marker of risk for depression, particularly during reward anticipation, even in the absence of (or accounting for) disrupted subjective mood. Further examinations of prospective associations between reward response and depression onset are needed.
Nelson River Pole 1 Thyristor Leakage Problem

The Nelson River HVDC system currently consists of two thyristor-based bipole schemes: Bipoles I and II. Pole 1 in Bipole I was found to have suffered from a serious thyristor leakage problem (TLP) after 20 years in service. In order to understand, evaluate, and resolve this problem, a comprehensive study was conducted in 2013 at Manitoba Hydro, which involved thyristor voltage monitoring, leakage current measurements, and simulations. The study revealed that the majority of thyristors in two of the three valve groups at both ends were leaky (i.e., exhibiting increased leakage currents) to various degrees. This paper provides an overview of the TLP and related investigation. The effects and symptoms/behaviors of the leaky thyristors are illustrated with the study results for one of the worst valves at each end. The failure mechanism of the leaky thyristors is also discussed. This paper should provide a clear understanding of the TLP from the user's perspective. A question, however, remains with regard to the root-cause of the TLP. Further research is required to answer this question.
Where We Fail: Location and Timing of Failure to Rescue in Trauma

Failure to rescue (FTR) is an outcome metric that reflects a center's ability to prevent mortality after a major complication. Identifying the timing and location of FTR events could help target efforts to reduce FTR rates. We sought to characterize the timing and location of FTR occurrences at our center, hypothesizing that FTR rates would be highest early after injury and in settings of lower intensity of care. We used data, prospectively collected from 2009 to 2013, on patients ≥16 years old with minimum Abbreviated Injury Score ≥2 from a single institution. Major complications (per Pennsylvania Trauma Systems Foundation definitions), mortality, and FTR rates were examined by location [prehospital, emergency department, operating room, intensive care unit (ICU), and interventional radiology] and by day post admission. Kruskal-Wallis and chi-squared tests were used to compare variables (P = 0.05). Major complications occurred in 899/6150 (14.6%) of patients [median age: 42, interquartile range (IQR): 25–57; 56% African American, 73% male, 76% blunt; median Injury Severity Score: 10, IQR: 5–17]. Of 899, 111 died (FTR = 12.4%). Compared with non-FTR cases, FTR cases had earlier complications (median day 1 (IQR: 0–4) versus 5 (IQR: 2–8), P < 0.001). FTR rates were highest in the prehospital (55%), emergency department (38%), and operating room (36%) settings, but the greatest number of FTR cases occurred in the ICU (52/111, 47%). FTR rates were highest early after injury, but the majority of cases occurred in the ICU. Efforts to reduce institutional FTR rates should focus on complications that occur in the ICU setting.
A FLUID INCLUSION IN A POROELASTIC SOLID WITH VOID COMPACTION

Summary The paper presents a study of the pressure development in a fluid inclusion located within a fluid-saturated poroelastic medium that can exhibit effects of void compaction. The void compaction introduces alterations in the deformability and fluid transport properties of the porous skeleton. A computational approach is used to examine the pressure rise in the fluid inclusion when the poroelastic medium is subjected to a far-field radial compression. The influence of void compaction on the magnitude and decay rate of the fluid pressure is illustrated through the computational simulation.
Thio-glucose bound gold nanoparticles enhance radio-cytotoxic targeting of ovarian cancer

The treatment of ovarian cancer has traditionally been intractable, and required novel approaches to improve therapeutic efficiency. This paper reports that thio-glucose bound gold nanoparticles (Glu-GNPs) can be used as a sensitizer to enhance ovarian cancer radiotherapy. The human ovarian cancer cells, SK-OV-3, were treated by gold nanoparticles (GNPs) alone, irradiation alone, or GNPs in addition to irradiation. Cell uptake was assayed using inductively coupled plasma atomic emission spectroscopy (ICP-AES), while cytotoxicity induced by radiotherapy was measured using both 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di-phenytetrazoliumromide and clonogenic assays. The presence of reactive oxygen species (ROS) was determined using CM-H2-DCFDA confocal microscopy and cell apoptosis was determined by an Annexin V-FITC/propidium iodide (PI) kit with flow cytometry. The cells treated by Glu-GNPs resulted in an approximate 31% increase in nanoparticle uptake compared to naked GNPs (p < 0.005). Compared to the irradiation alone treatment, the intracellular uptake of Glu-GNPs resulted in increased inhibition of cell proliferation by 30.48% for 90 kVp and 26.88% for 6 MV irradiation. The interaction of x-ray radiation with GNPs induced elevated levels of ROS production, which is one of the mechanisms by which GNPs can enhance radiotherapy on ovarian cancer.
FORMATION OF CELL MICROPATTERN BY NEWLY DEVELOPED HYDROGEL PROCESSING TECHNIQUE

This paper presents a novel hydrogel patterning technique that is similar to general micromachining technique. This technique permits the creating of cell micropatterns having arbitrary geometry because hydrogel materials having cell adhesiveness or non-adhesiveness can be patterned precisely. Also, this technique permits the process to culture surface during cultivation because all of the material such as hydrogel materials and hydrogel etching liquids are biological materials and doesn’t have cell cytotoxicity. Thus, cell micropatterns formed by different type cells can be created. This technique is going to be conducive to develop the fabrication of artificial three-dimensional cell tissue.
Role of breast reconstructive surgery in physical and emotional outcomes among breast cancer survivors.

BACKGROUND Tissue-sparing approaches to primary treatment and reconstructive options provide improved cosmetic outcomes for women with breast cancer. Earlier research has suggested that conservation or restitution of the breast might mitigate the negative effects of breast cancer on women's sexual well-being. Few studies, however, have compared psychosocial outcomes of women who underwent lumpectomy, mastectomy alone, or mastectomy with reconstruction. To address some of these issues, we examined women's adaptation to surgery in two large cohorts of breast cancer survivors. METHODS A total of 1957 breast cancer survivors (1-5 years after diagnosis) from two major metropolitan areas were assessed in two waves with the use of a self-report questionnaire that included a number of standardized measures of health-related quality of life, body image, and physical and sexual functioning. All P: values are two-sided. RESULTS More than one half (57%) of the women underwent lumpectomy, 26% had mastectomy alone, and 17% had mastectomy with reconstruction. As in earlier studies, women in the mastectomy with reconstruction group were younger than those in the lumpectomy or mastectomy-alone groups (mean ages = 50.3, 55.9, and 58.9, respectively; P: =.0001); they were also more likely to have a partner and to be college educated, affluent, and white. Women in both mastectomy groups complained of more physical symptoms related to their surgeries than women in the lumpectomy group. However, the groups did not differ in emotional, social, or role function. Of interest, women in the mastectomy with reconstruction group were most likely to report that breast cancer had had a negative impact on their sex lives (45.4% versus 29.8% for lumpectomy and 41.3% for mastectomy alone; P: =. 0001). CONCLUSIONS The psychosocial impact of type of primary surgery for breast cancer occurs largely in areas of body image and feelings of attractiveness, with women receiving lumpectomy experiencing the most positive outcome. Beyond the first year after diagnosis, a woman's quality of life is more likely influenced by her age or exposure to adjuvant therapy than by her breast surgery.
Crystallographic nature of deformation bands shown in Zn and Mg-based long-period stacking ordered (LPSO) phase

Formation of curious deformation bands has been reported as one of the deformation mechanisms occurring in an Mg-based long-period stacking ordered (LPSO) phase. The origin of the deformation band is still unknown, and the possibility of the deformation kink band and/or the deformation twin has been discussed. To clarify this, the crystallographic nature of deformation bands formed in the LPSO phase was examined by scanning electron microscope–electron backscatter diffraction (SEM-EBSD) pattern analysis. The results were compared to those of the deformation kink bands formed in hcp-Zn and deformation twins formed in hcp-Mg polycrystals. The deformation bands in the LPSO phase was confirmed not to exhibit a fixed crystal orientation relationship with respect to the matrix, different from the case shown in the deformation twin. Instead, the deformation band in the LPSO phase showed three arbitrariness on its crystallographic nature: an ambiguous crystal rotation axis that varied on the [0 0 0 1] zone axis from band to band; an arbitral crystal rotation angle that was not fixed and showed relatively wide distributions; and a variation in crystal rotation angle depending on the position even within a deformation band boundary itself. These features were coincident with those observed in the deformation bands formed in Zn polycrystals, suggesting that the formed deformation bands in LPSO phase crystals are predominantly deformation kink bands.
A model for automated rating of case law

The increasing volumes of case law available in publicly accessible databases cause serious problems if users are not able to filter on the authoritativeness of the decisions. In this paper we present a model by which large numbers of judgments can be rated, (nearly) without any human intervention. For most cases the legal importance of judgments can be derived from data on publication and citation, reflecting the opinion of the legal community. For newly rendered judgments endogenous variables are used, which turn out to be good predictors of authority.
Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity

Natural communities commonly contain many different species and functional groups, and multiple types of species interactions act simultaneously, such as competition, predation, commensalism or mutualism. However, experimental and theoretical investigations have generally been limited by focusing on one type of interaction at a time or by a lack of a common methodological and conceptual approach to measure species interactions. We compared four methods to measure and express species interactions. These approaches are, with increasing degree of model complexity, an extinction‐based model, a relative yield model and two generalized Lotka‐Volterra (LV) models. All four approaches have been individually applied in different fields of community ecology, but rarely integrated. We provide an overview of the definitions, assumptions and data needed for the specific methods and apply them to empirical data by experimentally deriving the interaction matrices among 11 protist and rotifer species, belonging to three functional groups. Furthermore, we compare their advantages and limitations to predict multispecies community dynamics and ecosystem functioning. The relative yield method is, in terms of final biomass production, the best method in predicting the 11‐species community dynamics from the pairwise competition experiments. The LV model, which is considering equilibrium among the species, suffers from experimental constraints given the strict equilibrium assumption, and this may be rarely satisfied in ecological communities. We show how simulations of a LV stochastic community model, derived from an empirical interaction matrix, can be used to predict multispecies community dynamics across multiple functional groups. Our work unites available tools to measure species interactions under one framework. This improves our ability to make management‐oriented predictions of species coexistence/extinction and to compare ecosystem processes across study systems.
IDEAL TAPER PREDICTION FOR BILLET CASTING

Mold taper is an important control parameter in the continuous casting of steel billets. Properly tapered mold walls compensate for shrinkage of the solidifying strand to maintain good contact and heat transfer between the mold wall and shell surface without exerting extra force on the hot and weak shell. The amount of taper needed varies with steel composition and casting conditions, such as mold length, casting speed, and type of lubrication. Inadequate mold taper leaves an air gap between the mold wall and shell surface which leads to a hotter and thinner shell within the mold. Ferrostatic pressure from the liquid core will bulge the weak shell within and out of the mold and even break out the shell in extreme situations. Excessive taper exerts extra load on the solidifying shell and increases dragging friction. Transverse cracks, shell buckling or even shell jamming and breakouts may occur. Past efforts conducted to assist mold taper prediction includes mathematical models to calculate thermal shrinkage of the steel billet [1-3] and thermal distortion of the mold . These previous investigations assume optimal taper should match the shell shrinkage, presuming this should produce good heat transfer across the interfacial layer between mold wall and billet surface at the face center along the mold axial direction. Corner effects have received little attention.
Effect of Hydrogen Sintering on Phase, Mechanical Property and High Temperature Response of Nanostructured W-60 at. % Cr Defense Alloy

Nanostructured W40Cr60 alloy was produced by mechanical alloying (MA) of elemental tungsten (W), chromium (Cr) powder in a high energy ball-mill followed by compaction at 250 MPa pressure and hydrogen sintering at 1500C for 5 h. The evolution of phase and microstructure of the milled powder and consolidated alloy was investigated by X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM). The crystallite size of W in W40Cr60 powder reduced from 100 μm at 0 h to 29 nm at 20 h of milling and lattice strain increases to 0.51% at 20 h of milling. The lattice parameter of tungsten shows initial expansion of lattice upto 0.22% at 5 h of milling and contraction of lattice upto 0.25% at 20 h of milling. The TEM observation revealed that the observed crystallite size (~20 nm) agrees well the measured crystallite size from XRD. Maximum solid solubility of 5.4 at. % Cr in W has been achieved at 20 h of milling. Hardness and Elastic Modulus of sintered W40Cr60 alloy are less compared to pure tungsten. Maximum wear depth and compressive strength of 54.33 m and 914 MPa respectively is achieved in sintered W40Cr60 alloy. Oxidation behavior of the sintered W40Cr60 alloy is also studied at 800°C for 15 h. Comparative study on the oxidation resistance of W, W70Cr30 and W40Cr60 alloy has been carried out to understand the high temperature behavior of pure W and W-Cr alloy. The research work shows encouraging results in terms of enhanced hardness and oxidation resistance as compared to recent study on nanostructured W-Cr alloys.
Exploiting dictionaries in named entity extraction: combining semi-Markov extraction processes and data integration methods

We consider the problem of improving named entity recognition (NER) systems by using external dictionaries---more specifically, the problem of extending state-of-the-art NER systems by incorporating information about the similarity of extracted entities to entities in an external dictionary. This is difficult because most high-performance named entity recognition systems operate by sequentially classifying words as to whether or not they participate in an entity name; however, the most useful similarity measures score entire candidate names. To correct this mismatch we formalize a semi-Markov extraction process, which is based on sequentially classifying segments of several adjacent words, rather than single words. In addition to allowing a natural way of coupling high-performance NER methods and high-performance similarity functions, this formalism also allows the direct use of other useful entity-level features, and provides a more natural formulation of the NER problem than sequential word classification. Experiments in multiple domains show that the new model can substantially improve extraction performance over previous methods for using external dictionaries in NER.
Optimizing Clinical Decision Support in the Electronic Health Record

Summary Objective Adoption of clinical decision support (CDS) tools by clinicians is often limited by workflow barriers. We sought to assess characteristics associated with clinician use of an electronic health record-embedded clinical decision support system (CDSS). Methods In a prospective study on emergency department (ED) activation of a CDSS tool across 14 hospitals between 9/1/14 to 4/30/15, the CDSS was deployed at 10 active sites with an on-site champion, education sessions, iterative feedback, and up to 3 gift cards/clinician as an incentive. The tool was also deployed at 4 passive sites that received only an introductory educational session. Activation of the CDSS – which calculated the Pulmonary Embolism Severity Index (PESI) score and provided guidance – and associated clinical data were collected prospectively. We used multivariable logistic regression with random effects at provider/facility levels to assess the association between activation of the CDSS tool and characteristics at: 1) patient level (PESI score), 2) provider level (demographics and clinical load at time of activation opportunity), and 3) facility level (active vs. passive site, facility ED volume, and ED acuity at time of activation opportunity). Results Out of 662 eligible patient encounters, the CDSS was activated in 55%: active sites: 68% (346/512); passive sites 13% (20/150). In bivariate analysis, active sites had an increase in activation rates based on the number of prior gift cards the physician had received (96% if 3 prior cards versus 60% if 0, p<0.0001). At passive sites, physicians < age 40 had higher rates of activation (p=0.03). In multivariable analysis, active site status, low ED volume at the time of diagnosis and PESI scores I or II (compared to III or higher) were associated with higher likelihood of CDSS activation. Conclusions Performing on-site tool promotion significantly increased odds of CDSS activation. Optimizing CDSS adoption requires active education. Citation: Ballard DW, Vemula R, Chettipally UK, Kene MV, Mark DG, Elms AK, Lin JS, Reed ME, Huang J, Rauchwerger AS, Vinson DR, for the KP CREST Network Investigators. Optimizing clinical decision support in the electronic health record – clinical characteristics associated with the use of a decision tool for disposition of ED patients with pulmonary embolism.
Fitness activity classification by using multiclass support vector machines on head-worn sensors

Fitness activity classification on wearable devices can provide activity-specific information and generate more accurate performance metrics. Recently, optical head-mounted displays (OHMD) like Google Glass, Sony SmartEyeglass and Recon Jet have emerged. This paper presents a novel method to classify fitness activities using head-worn accelerometer, barometric pressure sensor and GPS, with comparisons to other common mounting locations on the body. Using multiclass SVM on head-worn sensors, we obtained an average F-score of 96.66% for classifying standing, walking, running, ascending/descending stairs and cycling. The best sensor location combinations were found to be on the ankle plus another upper body location. Using three or more sensors did not show a notable improvement over the best two-sensor combinations.