Miracle-dz/UniFAR-FTUs huggingface dataset:
Variations in rates of tracheostomy in the critically ill trauma patient*

Objective:The utility of tracheostomy to expedite weaning and prevent complications in patients with acute respiratory failure is actively debated, with many physicians holding strong opinions regarding the value and timing of this intervention. We postulated that these opinions would be reflected in significant variation in tracheostomy rates across centers. Thus, we set out explore the extent and potential sources of this variation among injured patients cared for in trauma centers in the United States. Design:This is a retrospective cohort study. We used stratification and hierarchical multivariate analysis to evaluate the effect of patient and institutional characteristics on tracheostomy rates and variance decomposition to determine the proportion of variance across institutions explained by patient characteristics. Setting:Intensive care units within trauma centers participating in the National Trauma Databank. Patients:Injured patients admitted over the years 2001–2003, age ≥16 yrs, with an Injury Severity Score ≥9 and a diagnosis of acute respiratory failure, excluding patients with burn injuries and those with a severe injury to the face or neck who might require tracheostomy for maintenance of an airway. Interventions:None. Measurements and Main Results:There were 17,523 patients meeting inclusion criteria: 4,146 (24%) underwent tracheostomy. The mean tracheostomy rate across centers was 19.6 per 100 hospital admissions with a range of 0–59. This variation persisted after stratification by age, injury mechanism, and severity. Although several patient and injury characteristics were predictive of tracheostomy, there were no identifiable institutional characteristics associated with tracheostomy. Patient characteristics accounted for only 14% of the variance across centers. Conclusions:There is significant unexplained variation in the rates of tracheostomy in critically injured patients with acute respiratory failure. This variation might reflect preconceived notions of efficacy among physicians practicing in the absence of evidence to guide care. The variation provides evidence of equipoise and emphasizes the need for a well-conducted randomized controlled trial to evaluate the utility of this procedure.
Immunohistochemical toolkit for tracking and quantifying xenotransplanted human stem cells.

AIM Biomarker-based tracking of human stem cells xenotransplanted into animal models is crucial for studying their fate in the field of cell therapy or tumor xenografting. MATERIALS & METHODS Using immunohistochemistry and in situ hybridization, we analyzed the expression of three human-specific biomarkers: Ku80, human mitochondria (hMito) and Alu. RESULTS We showed that Ku80, hMito and Alu biomarkers are broadly expressed in human tissues with no or low cross-reactivity toward rat, mouse or pig tissues. In vitro, we demonstrated that their expression is stable over time and does not change along the differentiation of human-derived induced pluripotent stem cells or human glial-restricted precursors. We tracked in vivo these cell populations after transplantation in rodent spinal cords using aforementioned biomarkers and human-specific antibodies detecting apoptotic, proliferating or neural-committed cells. CONCLUSION This study assesses the human-species specificity of Ku80, hMito and Alu, and proposes useful biomarkers for characterizing human stem cells in xenotransplantation paradigms.
Sources of Nitrite in Streams of an Intensively Cropped Watershed

The sources of high in‐stream nitrite (NO2−) concentrations were investigated in two major streams located in an intensively cropped watershed in Quebec, Canada. Nitrogen retention was determined to evaluate the dynamics in relation to nitrogen transport along both stream branches during summer‐low‐water and fall‐recharge regimes. In the first stream branch, NO2− and ammonium (NH4+) showed removal patterns during summer‐low‐water and fall‐recharge periods, whereas, in the second branch, NO2− and NH4+ exports occurred during both hydrologic regimes. The study also demonstrated that seepage water is a source of NO2− in‐stream, which varies within the watershed stream branches and with the hydrologic regime. The results highlighted a significant reductive microbial activity in seepage water from either denitrification or dissimilatory nitrate reduction to ammonium (DNRA), leading to nitrate (NO3−) consumption. Differences in groundwater NO3− concentrations feeding each stream branch may have significantly influenced NH4+ and NO2− concentrations found in seepage water, which potentially resulted in quantitatively significant NO2− formation.
A genetic circuit amplifier: design and simulation

A genetic circuit amplifier is designed using an electronic inverting amplifier as a starting point. Two simulation methods are used to analyze circuit performance in terms of the impulse and sinusoidal responses of electrical engineering. The first method is an exact stochastic simulation based on a kinetic model of the circuit. The second method incorporates statistical thermodynamic analysis. The simulations are used to analyze amplifier performance in response to classical systems analysis stimuli: impulses and sine waves. Degradation reactions, analogous to leakage off circuit capacitors, are found to have considerable impact on circuit response. For the nonlinear gain element used in our exemplary circuit, the selection of bias level based on controlling protein degradation rate plays an important role in determining circuit behavior. A parameter without electronic analog, the circuit plasmid copy number, is crucial to circuit operation. These simulations suggest that the copy number must be less than 50 for desired circuit operation.
NEGF based transport modelling with a full-band, pseudopotential Hamiltonian: Theory, implementation and full device simulations

This paper presents the theory, implementation and application of a new quantum transport, NEGF based modelling approach employing a full-band Empirical Pseudopotential (EP) Hamiltonian. The use of a hybrid real-space/plane-waves basis results in a remarkable reduction of the computational burden compared to a full plane waves basis, which allowed us to obtain complete, self-consistent simulations for both FETs and Tunnel FETs in Si or in Ge, and with geometrical features in line with forthcoming CMOS technologies.
Mining semantic trajectories

A typical problem in the field of moving object MO databases consists in discovering interesting trajectory patterns. To solve this problem, data mining techniques are commonly used. Due to the huge volume of these trajectory data, some form of compression facilitates the data processing. One of such compression techniques is based on the notion of stops and moves. In this approach, a set of places that are relevant to the application, denoted Places of Interest POIs is selected. If a moving object spends a pre-defined amount of time in a place of interest, this place is considered a stop for the object's trajectory. Thus, raw trajectories given by O_{id}, t, x, y-tuples can be replaced by a sequence of application-relevant stops. This leads to the concept of semantic trajectory, in short, a trajectory obtained by replacing raw trajectory data with a sequence of stops, and enriched with metadata of the POIs corresponding to such stops. We present a language based on regular expressions over constraints, denoted RE-SPaM, that can intensionally express sequential patterns. The constraints in RE-SPaM are defined as conjunctions of equalities over metadata of the POIs. In addition, we introduce a data mining algorithm, based on sequential pattern mining techniques, where uninteresting sequences are pruned in advance making use of the automaton that accepts a RE-SPaM expression. This makes the task of the analyst easier, and the mining algorithm more efficient. We also show that RE-SPaM can be extended to support spatial functions, thus integrating spatial data in a moving object setting proposals so far only account for the MO trajectories themselves. We denote the resulting language RE-SPaM^{+S}. We show that the overhead of this extension is negligible, due to caching techniques that we explain in the paper. We close the paper with a case study over which we perform experiments to study the main variables that impact the performance of the mining algorithm.
Combination of Tigecycline and N-Acetylcysteine Reduces Biofilm-Embedded Bacteria on Vascular Catheters

ABSTRACT To assess the efficacy of an antibiofilm/antimicrobial agent combination, we incubated catheter segments colonized with one of six studied bacterial organisms in N-acetylcysteine, tigecycline, N-acetylcysteine-tigecycline, or saline. Segments were washed, sonicated, and cultured. N-acetylcysteine-tigecycline significantly decreased all viable biofilm-associated bacteria and was synergistic for methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis.
PAAS: A system level simulator for heterogeneous computing architectures

Heterogeneous computing with hardware accelerators is a promising direction to overcome the power and performance walls in traditional computing systems. CPU-accelerator integrated architectures, such as CPU with ASIC or FPGA based accelerators, are able to provide customized processing according to application requirements and are thus particularly attractive to speed up computation-intensive applications. Therefore, system level simulation showing the interaction among CPUs, hardware accelerators and memory system precisely is important for performing design space exploration leading to architecture and design optimization. In this work, we present PAAS (Processor Accelerator Architecture Simulator), a system level simulator to enable cycle-accurate full system simulation of CPU-accelerator heterogeneous systems. PAAS can easily support flexible architectural configurations, such as different on-chip interconnection topologies, memory hierarchy, etc. Using PAAS, this paper also presents the analysis of the impact of different architectural configurations on the performance of benchmark applications with different execution characteristics using FPGA based accelerators. Furthermore, as an example showing the research capability of PAAS, this paper proposes and investigates a cache-partitioning scheme for improving the performance of shared-cache based CPU-FPGA systems.
English-Turkish Parallel Treebank with Morphological Annotations and its Use in Tree-based SMT

In this paper, we report our tree based statistical translation study from English to Turkish. We describe our data generation process and report the initial results of tree-based translation under a simple model. For corpus construction, we used the Penn Treebank in the English side. We manually translated about 5K trees from English to Turkish under grammar constraints with adaptations to accommodate the agglutinative nature of Turkish morphology. We used a permutation model for subtrees together with a word to word mapping. We report BLEU scores under simple choices of inference algorithms.
Differential Expression of Two Paralogous Genes of Bacillus subtilis Encoding Single-Stranded DNA Binding Protein

ABSTRACT The Bacillus subtilis genome comprises two paralogous single-stranded DNA binding protein (SSB) genes, ssb and ywpH, which show distinct expression patterns. The main ssb gene is strongly expressed during exponential growth and is coregulated with genes encoding the ribosomal proteins S6 and S18. The gene organization rpsF-ssb-rpsR as observed in B. subtilis is found in many gram-positive as well as some gram-negative bacteria, but not in Escherichia coli. The ssb gene is essential for cell viability, and like other SSBs its expression is elevated during SOS response. In contrast, the paralogous ywpH gene is transcribed from its own promoter at the onset of stationary phase in minimal medium only. Its expression is ComK dependent and its gene product is required for optimal natural transformation.
Bile acid transport systems as pharmaceutical targets

Drug targeting aims to improve the therapeutic index of a drug, i.e. to maximize the ratio between the desired pharmacological action and adverse sideeffects. This requires the achievement of a high drug concentration in the target organ of the body. As direct application of the drug to the target organ is rare, the drug has to be administered systemically. For chronic diseases requiring long-term or lifetime treatment, non-invasive drug application is necessary. Specific problems with peptide and protein drugs are their low permeability through biological membranes, their negligible intestinal absorption and their susceptibility to enzymatic hydrolysis. Drug targeting implies, at a molecular level, specific recognition and uptake of the drug by the target tissue, and thus three molecular characteristics are important for drug delivery: the drug molecule, the drug carrier; and the molecular recognition signals. Ideally, all three factors are combined in a small drug molecule [1-3], but in most cases the drug carrier should mediate specific recognition at the target cells. The liver occupies a central role in the metabolism of drugs, and many pathological states are unique to this organ, such as liver infections (hepatitis, malaria, leishmaniasis, etc.), lipid disorders, cirrhosis, metabolic disorders, storage disease or hepatobiliary carcinomas. None of these diseases can be treated satisfactorily by current pharmacological drugs, because of either lack of active drugs or limitations due to adverse side-effects in extrahepatic tissues. It is essential that drugs used to treat these diseases should be liver specific. Many drugs by themselves reach relatively high concentrations in the liver as a result of a high first-pass effect.
Hybrid filter with CPPM for Suppression of Common Mode Voltage and Differential Mode Harmonics in Three Phase PV Inverter

In Pulse Width Modulation (PWM) Inverters, the peaks of output Common Mode Voltage (CMV) are very high due to the instantaneous imbalance of 3Phase Voltages. The CMV will produce a huge pulsating Common Mode Current (CMC) through the distributed capacitance of the system and will cause the high shaft voltage leads to damage of the motor bearing. The CMC could interfere with the adjacent devices along the ground wire and even will result in the wrong operation of the devices. The Differential Mode (DM) is conducted on the signal line and ground line in the opposite direction to each other, which causes harmonics there by noise in the line and will, distorts the system. In this paper, a Hybrid filter is used to reduce the CMV and DM harmonics in a three-phase inverter with Carrier Peak Position Modulation (CPPM). In the proposed scheme, hybrid filter is implemented for Photovoltaic (PV) based inverter fed 3-Phase Induction motor with a modified RCC MPPT technique. The above scheme is implemented in Simulink environment of the MATLAB.
[The effects of smoking].

What is in a cigarette? What you need to know • Worldwide, tobacco use causes nearly 6 million deaths per year • Current trends show that tobacco use will cause more than 8 million deaths annually by 2030 • On average, smokers die 10 years earlier than nonsmokers. • More deaths are caused each year by tobacco use than by all deaths from human immunodeficiency virus (HIV), illegal drug use, alcohol use, motor vehicle injuries, suicides, and murders combined. • Smoking causes an estimated 90% of all lung cancer deaths in men and 80% of all lung cancer deaths in women. • An estimated 90% of all deaths from chronic obstructive lung disease are caused by smoking.
Addition of home-based cognitive retraining to treatment as usual in first episode schizophrenia patients: A randomized controlled study

Objective: We examined the effectiveness of a 2-month-long home-based cognitive retraining program together with treatment as usual (TAU; psychoeducation and drug therapy) on neuropsychological functions, psychopathology, and global functioning in patients with first episode schizophrenia (FES) as well as on psychological health and perception of level of family distress in their caregivers. Materials and Methods: Forty-five FES patients were randomly assigned to either treatment group receiving home-based cognitive retraining along with TAU (n=22) or to control group receiving TAU alone (n=23). Patients and caregivers received psychoeducation. Patients and one of their caregivers were assessed for the above parameters at baseline, post-assessment (2 months) and at 6-months follow-up assessment. Results: Of the 45 patients recruited, 12 in the treatment group and 11 in the control group completed post-intervention and follow-up assessments. Addition of home-based cognitive retraining along with TAU led to significant improvement in neuropsychological functions of divided attention, concept formation and set-shifting ability, and planning. Effect sizes were large, although the sample size was small. Conclusions: Home-based cognitive retraining program has shown promise. However, further studies examining this program on a larger cohort with rigorous design involving independent raters are suggested.
Effect of polyriboinosinic-polyribocytidylic acid and antibody on infection of immunosuppressed mice with vaccinia virus.

The effects were studied of polyriboinosinic-polyribocytidylic acid (poly I:C) and specific antiviral antibody on the course of fatal systemic vaccinia virus infection in immunosuppressed mice. Administration of a single dose of vaccinia-immune serum was more effective in protecting Cytoxan-treated mice on day 3 or day 4 after infection with vaccinia virus than were four daily doses of poly I:C begun on the same day. An antiviral effect of poly I:C, as determined by lower levels of viremia, was present within 24 hr after initiation of therapy with poly I:C. Combined therapy with poly I:C and antibody was considerably more effective than therapy with either of these agents alone when administered late in the course of this systemic infection. This suggests that combined therapy with an inducer of interferon and specific antibody to the virus might be effective in immunologically incompetent hosts with severe viral infections.
Characterization of cuticular chitin‐binding proteins of Leptinotarsa decemlineata (Say) and post‐ecdysial transcript levels at different developmental stages

Seven cuticle chitin‐binding proteins (Ld‐CP1v1 to 7) were deduced from antenna cDNAs of adult Colorado potato beetles, Leptinotarsa decemlineata (Say), based on their consensus sequences. The mature proteins consisted of 87–188 residues. Ld‐CP1v1 formed a distinct orthologous protein cluster (OP1) along with four proteins from other insect species in a neighbor‐joining phylogenetic tree. These proteins also contained a proline glutamine‐rich (PQ‐rich) region and a highly conserved C‐terminal motif (Phr). Their consensus region lacked the defined aromatic triad. Ld‐CP2 to 6 clustered with those bearing RR‐1 consensus and Ld‐CP7 with RR‐2 consensus. Ld‐CP1v1 to 4 were expressed at the post‐ecdysial period in all the developmental stages whereas Ld‐CP5 to 7 were expressed mainly in adults.
NEW ASPECTS OF THE MESOLITHIC‐NEOLITHIC CEMETERIES AND SETTLEMENT AT ZVEJNIEKI, NORTHERN LATVIA

The paper reflects upon recent international research at Zvejnieki in northern Latvia, a renowned complex of a burial ground and two settlement sites used in the Mesolithic and Neolithic. Since its discovery and first excavations in the 1960s, Zvejnieki continues to produce evidence that provides new grounds for understanding mortuary practises and ancient lifeways. This information is relevant for other contemporary sites in Europe revealing new and hitherto unexpected elements of burial traditions. It is suggested that the Zvejnieki population was partly mobile, and the site was one of the places to bury the dead. The ancestral link was established through transportation and use of occupational debris from more ancient sites and through the incorporation of earlier burial space or even burials into the new graves. The depth of a burial also appears to be a significant variable in ancient mortuary practices. (Less)
Sustaining the Earth's Watersheds-Agricultural Research Data System: Overview of development and challenges

The USDA Agricultural Research Service has supported watershed research since the 1930s. Data from USDA Agricultural Research Service watersheds have been disseminated independently at each location, hindering multi-site analyses. A virtual team spanning diverse organizational units developed a web-based system, Sustaining the Earth's Watersheds-Agricultural Research Data System (STEWARDS) that allows users to search, visualize, and download soil, water, climate, management, and economic data from Conservation Effects Assessment Project benchmark watersheds. The objective of this paper is to provide an overview of STEWARDS and discuss challenges that were met to deliver STEWARDS on time, according to requirements, and within available resources. The information technology specialists had to understand that vague and changing requirements are reasonable for a system to support loosely coupled research across diverse watersheds. Researchers and data managers had to learn to communicate clearly about their data. Open communication, respect for perspectives and constraints of others, and a shared commitment to the goal provided the basis for trust. Anticipated benefits of STEWARDS include data preservation, increased data use, and facilitation of hydrological research.
Underwater flight by the planktonic sea butterfly

ABSTRACT In a remarkable example of convergent evolution, we show that the zooplanktonic sea butterfly Limacina helicina ‘flies’ underwater in the same way that very small insects fly in the air. Both sea butterflies and flying insects stroke their wings in a characteristic figure-of-eight pattern to produce lift, and both generate extra lift by peeling their wings apart at the beginning of the power stroke (the well-known Weis-Fogh ‘clap-and-fling’ mechanism). It is highly surprising to find a zooplankter ‘mimicking’ insect flight as almost all zooplankton swim in this intermediate Reynolds number range (Re=10–100) by using their appendages as paddles rather than wings. The sea butterfly is also unique in that it accomplishes its insect-like figure-of-eight wing stroke by extreme rotation of its body (what we call ‘hyper-pitching’), a paradigm that has implications for micro aerial vehicle (MAV) design. No other animal, to our knowledge, pitches to this extent under normal locomotion. Highlighted Article: The zooplanktonic sea butterfly Limacina helicina ‘flies’ underwater using many of the same fluid dynamic ‘tricks’ that very small insects use to fly in air.