Miracle-dz/UniFAR-FTUs huggingface dataset:
First Transcriptome of the Testis-Vas Deferens-Male Accessory Gland and Proteome of the Spermatophore from Dermacentor variabilis (Acari: Ixodidae)

Ticks are important vectors of numerous human diseases and animal diseases. Feeding stimulates spermatogenesis, mating and insemination of male factors that trigger female reproduction. The physiology of male reproduction and its regulation of female development are essentially a black box. Several transcriptomes have catalogued expression of tick genes in the salivary glands, synganglion and midgut but no comprehensive investigation has addressed male reproduction and mating. Consequently, a new global approach using transcriptomics, proteomics, and quantitative gene expression is needed to understand male reproduction and stimulation of female reproduction. This first transcriptome to the reproductive biology of fed male ticks, Dermacentor variabilis, was obtained by 454 pyrosequencing (563,093 reads, 12,804 contigs). Gene Ontology (Biological Processes level III) recognized 3,866 transcripts in 73 different categories; spermiogenesis; spermatogenesis; peptidases, lipases and hydrolases; oxidative and environmental stress; immune defense; and protein binding. Reproduction-associated genes included serine/threonine kinase, metalloendoproteinases, ferritins, serine proteases, trypsin, cysteine proteases, serpins, a cystatin, GPCR and others. qRT-PCR showed significant upregulation from unfed versus fed adult male reproductive organs of zinc metalloprotease, astacin metalloprotease and serine protease, enzymes important in spermiogenesis and mating activity in insects, as well as a GPCR with the greatest similarity to a SIFamide receptor known to be important in regulating courtship behavior in Drosophila. Proteomics on these organs and the spermatophore by tryptic digestion/Liquid chromatography/Mass spectrometry/Mass spectrometry (LC/MS/MS) demonstrated expression of many of the same messages found by 454 sequencing, supporting their identification, and revealed differences in protein distribution in the reproductive system versus the spermatophore. We found Efα but no EF β in the transcriptome and neither of these proteins in the spermatophore. Thus, the previously described model for male regulation of female reproduction may not apply to other ticks. A new paradigm is needed to explain male stimulation of female tick reproduction.
A flexible coefficient smooth transition time series model

We consider a flexible smooth transition autoregressive (STAR) model with multiple regimes and multiple transition variables. This formulation can be interpreted as a time varying linear model where the coefficients are the outputs of a single hidden layer feedforward neural network. This proposal has the major advantage of nesting several nonlinear models, such as, the self-exciting threshold autoregressive (SETAR), the autoregressive neural network (AR-NN), and the logistic STAR models. Furthermore, if the neural network is interpreted as a nonparametric universal approximation to any Borel measurable function, our formulation is directly comparable to the functional coefficient autoregressive (FAR) and the single-index coefficient regression models. A model building procedure is developed based on statistical inference arguments. A Monte Carlo experiment showed that the procedure works in small samples, and its performance improves, as it should, in medium size samples. Several real examples are also addressed.
Comparison of Photopic Negative Response of Full-Field and Focal Electroretinograms in Detecting Glaucomatous Eyes

Purpose. To compare the photopic negative response (PhNR) of the full-field electroretinogram (ERG) to the PhNR of the focal ERGs in detecting glaucoma. Methods. One hundred and three eyes with glaucoma and 42 normal eyes were studied. Full-field ERGs were elicited by red stimuli on a blue background. The focal ERGs were elicited by a 15° white stimulus spot centered on the macula, the superotemporal or the inferotemporal areas of the macula. Results. In early glaucoma, the areas under the receiver operating characteristic curves (AUCs) were significantly larger for the focal PhNR (0.863–0.924) than those for the full-field PhNR (0.666–0.748) (P < .05). The sensitivity was significantly higher for the focal PhNR than for the full-field PhNR in early (P < .01) and intermediate glaucoma (P < .05). In advanced glaucoma, there was no difference in the AUCs and sensitivities between the focal and full-field PhNRs. Conclusions. The focal ERG has the diagnostic ability with higher sensitivity in detecting early and intermediate glaucoma than the full-field ERG.
Force health protection: essential element of combat readiness.

Mosquito surveillance records from the US Army Public Health Command Region-West (APHCR-W) were georeferenced and made available online via the database mapping application MosquitoMap (www.mosquitomap.org). This article briefly reviews the history of the APHCR-W surveillance program and some characteristics of the resulting dataset, which numbers over 100,000 records mainly from US Department of Defense (DoD) facilities in the western United States from 1947 to 2009. The value of past and future DoD mosquito surveillance efforts can be increased by reporting the location of collection data in online spatial databases such as MosquitoMap. *http://earthobservatory.nasa. gov/Features/MeasuringVegetation/measuring_vegetation_2. php †http://phc.amedd. army.mil/topics/phcrspecific/west/Pages/default.aspx
On the Rapid Intensification of Hurricane Wilma (2005). Part I: Model Prediction and Structural Changes

AbstractIn this study, a 72-h cloud-permitting numerical prediction of Hurricane Wilma (2005), covering its initial 18-h spinup, an 18-h rapid intensification (RI), and the subsequent 36-h weakening stage, is performed using the Weather Research Forecast Model (WRF) with the finest grid length of 1 km. The model prediction uses the initial and lateral boundary conditions, including the bogus vortex, that are identical to the Geophysical Fluid Dynamics Laboratory’s then-operational data, except for the time-independent sea surface temperature field. Results show that the WRF prediction compares favorably in many aspects to the best-track analysis, as well as satellite and reconnaissance flight-level observations. In particular, the model predicts an RI rate of more than 4 hPa h−1 for an 18-h period, with the minimum central pressure of less than 889 hPa. Of significance is that the model captures a sequence of important inner-core structural variations associated with Wilma’s intensity changes, namely, fro.
Bringing up OpenSky: A large-scale ADS-B sensor network for research

Automatic Dependent Surveillance-Broadcast (ADS-B) is one of the key components of the next generation air transportation system. Since ADS-B will become mandatory by 2020 for most airspaces, it is important that aspects such as capacity, applications, and security are investigated by an independent research community. However, large-scale real-world data was previously only accessible to a few closed industrial and governmental groups because it required specialized and expensive equipment. To enable researchers to conduct experimental studies based on real data, we developed OpenSky, a sensor network based on low-cost hardware connected over the Internet. OpenSky is based on off-the-shelf ADS-B sensors distributed to volunteers throughout Central Europe. It covers 720,000 km2, is able to capture more than 30% of the commercial air traffic in Europe, and enables researchers to analyze billions of ADS-B messages. In this paper, we report on the challenges we faced during the development and deployment of this participatory network and the insights we gained over the last two years of operations as a service to academic research groups. We go on to provide real-world insights about the possibilities and limitations of such low-cost sensor networks concerning air traffic surveillance and further applications such as multilateration.
Yield and Economics of Rabi Sorghum [Sorghum bicolor (L.) Moench] as Influenced by Different Drip Irrigation Regimes and Fertigation Levels

Sorghum [Sorghum bicolor (L.) Moench], a C4 plant is known as great millet, durra, jowari or milo and is cultivated widely in tropical and sub-tropical regions. Global sorghum area trends indicated that area increased from 45 million ha in 1970s to 51 million ha in 1980s. Later there was fluctuation in area by 4 to 10 million ha and it declined to 42.12 million ha by 2012-13. Grain yields have increased from 1129 kg ha -1 in 1970s to 1457 kg ha -1 in 201213 (FAO, 2013) and the sorghum area occupied in 2016 globally was around 42 million hectares with the production and productivity of about 63.08 m tonnes and 1.60 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 03 (2018) Journal homepage: http://www.ijcmas. com
In Vitro Study on Contribution of Oxidative Metabolism of Isolated Rabbit Heart Mitochondria to Myocardial Reperfusion Injury

The present study was performed to clarify oxygen-induced damage following myocardial reperfusion, using three mitochondrial preparations from isolated rabbit hearts (non-ischemic hearts and those subjected to 40 and 90 minutes of normothermic global ischemia). The viability of mitochondria was evaluated by adenosine triphosphate generation. The extent of mitochondrial injury produced by reactive oxygen metabolism was assessed by the intensity of hydroxyl radical signal detected with electron spin resonance spectroscopy and the reduction of coenzyme Q10 level. The greatest oxygen-induced injury was observed in 40-minute ischemic mitochondria exposed to pure oxygen. The use of superoxide dismutase and catalase satisfactorily prevented the oxygen-induced injury. Moreover, the net adenosine triphosphate generation of the 40-minute ischemic mitochondria was comparable to that of the nonischemic mitochondria without the enzymes. These results suggest that reperfusion of the ischemic myocardium with viable mitochondria is deleterious, because mitochondria are susceptible to injury resulting from oxidative metabolism, and that the use of superoxide dismutase, together with catalase, is beneficial for the restoration of cardiac function after ischemia.
Online Data Collection from Video Game Players: Methodological Issues

The paper outlines the advantages and disadvantages of using the Internet to collect data concerning both online and offline gamers. Drawing from experience of a number of studies carried out online by the authors and by reviewing the available literature, the authors discuss the main issues concerning data collected from video game players. The paper examines a number of areas, including recruiting and utilizing participants, validity, suitable methods of data collection (i.e., questionnaire studies, online tests, participant observation, online interviews), and ethical issues. It is concluded that online research methods can be a useful way of examining the psychosocial aspects of video game playing.
Enhancing Detection Model for Multiple Hypothesis Tracking

Tracking-by-detection has become a popular tracking paradigm in recent years. Due to the fact that detections within this framework are regarded as points in the tracking process, it brings data association ambiguities, especially in crowded scenarios. To cope with this issue, we extended the multiple hypothesis tracking approach by incorporating a novel enhancing detection model that included detection-scene analysis and detection-detection analysis; the former models the scene by using dense confidential detections and handles false trajectories, while the latter estimates the correlations between individual detections and improves the ability to deal with close object hypotheses in crowded scenarios. Our approach was tested on the MOT16 benchmark and achieved competitive results with current state-of-the-art trackers.
Automated watershed subdivision for simulations using multi-objective optimization

ABSTRACT A qualitative trial-and-error approach is commonly used to define watershed subdivisions through varying a single topographic threshold value. A methodology has been developed to quantitatively determine spatially variable threshold values using topography and a user-defined landscape reference layer. Optimization and topographic parameterization algorithms were integrated to create solutions that minimize the number of sub-watersheds and maximize the agreement between the discretized watershed and the reference layer. The system was evaluated using different reference datasets such as soil type, land management, and landscape form. Comparison of simulated results indicated that the scenario using land management as the reference layer yielded results closer to the scenario subdivided using a constant topographic threshold but with approximately 10 times more sub-catchments and therefore indicating customization of the watershed subdivision to the user-defined reference layer. The proposed optimization technology could be used in adequately applying watershed modeling technology in developing conservation practice implementation plans.
Long-term follow-up and amputation-free survival in 497 casualties with combat-related vascular injuries and damage-control resuscitation

BACKGROUND The effectiveness of damage-control resuscitation (DCR) has been demonstrated in recent US conflicts. Wartime casualties treated for hemorrhagic shock from vascular wounds were studied to report the 24-hour transfusion requirements, graft patency, and amputation-free survival for major vascular injuries. METHODS Joint Theater Trauma Registry data from August 2006 to April 2011 (56 months) were retrospectively reviewed. Included were casualties with a vascular injury who presented to US combat support hospitals in Iraq or Afghanistan. Amputation-free survival and graft patency were determined from record and imaging review. RESULTS The study group consisted of 497 severely wounded local national and military casualties (mean [SD] Injury Severity Score [ISS], 17 [8.5]) presenting with acidosis (pH 7.29 [0.15]), tachycardia (heart rate, 110 [29.31]), and coagulopathy (international normalized ratio, 1.6 [2.33]). Given DCR and early management of vascular injury, blood pressure, heart rate, temperature, hemoglobin, and base deficit improved promptly (p < 0.05) by intensive care unit admission. Transfusion requirements included packed red blood cells (15 [13] U; range, 1–70 U), fresh frozen plasma (14 [13] U; range, 1–72 U), cryoprecipitate (13 [15] U; range, 1–49 U), and platelets (8 [6] U; range, 1–36 U). Mean operative time was 232 minutes (range, 16–763 minutes). US casualties (n = 111) had limb salvage attempted for 113 extremity vascular injuries (3 [2%] iliac, 33 [30%] femoral, 23 [20%] popliteal, 13 [12%] tibial, 33 [30%] brachial, 4 [3%] ulnar, and 4 [(3%] radial). In this subgroup, 28 (25%) were revascularized by a primary repair or end anastomosis, 80 (71%) were revascularized by saphenovenous grafts, and 5 (4%) were revascularized by prosthetic grafts. The follow-up ranged from 29 days to 1,079 days, (mean, 347 days), during which 96 grafts (84.9%) remained patent, 16 casualties (14.2%) required a delayed amputation, and 110 (99.1%) survived. Popliteal injuries had the highest amputation rate (7 of 23, 30.4%). The amputation-free survival was 84%. CONCLUSION In severely wounded casualties, wartime surgical strategies to save both life and limb evidently permit definitive procedures at initial surgery with excellent limb salvage results. This outcome analysis in a large cohort can help to refine surgical judgment and support contemporary DCR practices for major vascular injury. LEVEL OF EVIDENCE Epidemiologic study, level III; therapeutic study, level V.
Breakthrough Febrile Neutropenia and Associated Complications in Non-Hodgkin’s Lymphoma Patients Receiving Pegfilgrastim

Background: Febrile neutropenia (FN) is a dose-limiting complication of chemotherapy. Judicious usage of prophylactic granulocyte-colony-stimulating factors, such as pegfilgrastim, can prevent the occurrence of FN. Although studies have been conducted to evaluate the effectiveness of pegfilgrastim to prevent FN in lymphoma patients receiving myelosuppressive chemotherapy, limited data is available to identify patients who are at risk of developing FN despite primary prophylaxis with pegfilgrastim (breakthrough FN). Objectives: The aim of this study is to: (1) identify clinical characteristics of patients who develop breakthrough FN, and (2) provide descriptive data on the incidence of breakthrough FN among lymphoma patients. Methods: This is a single-centre, retrospective cohort study. Non-Hodgkin’s lymphoma patients who received CHOP-based chemotherapy with pegfilgrastim between January 2007 and May 2009 were identified through the Singapore Lymphoma Registry. Patient demographics, past and present medical history, cancer treatment history and laboratory parameters were collected from electronic databases and medical records. In this study, patients did not receive oral antibiotic prophylaxis along with chemotherapy. Results: A total of 132 patients were included in the final analysis. Median age of patients was 55 years. The incidence of breakthrough FN among patients in cycle 1 and across all cycles was 4.5% and 13.6%, respectively (n = 132). 3.3% (n = 60) of the patients receiving dose-dense chemotherapy had breakthrough FN, and this was 22.2% (n = 72) in patients receiving standard dose chemotherapy. Administration of chemotherapy every 21 days (adjusted OR = 12.1, p = 0.009) and patients with positive blood cultures (adjusted OR = 18.1, p = 0.001) were strongly associated with the occurrence of breakthrough FN. Conclusion: Despite routine administration of pegfilgrastim with CHOP chemotherapy, a high proportion of patients experienced FN after chemotherapy. Identifying patients at risk for breakthrough FN events may allow the optimization of myeloid growth factor usage among lymphoma patients receiving chemotherapy.
Size-controllable synthesis of bare gold nanoparticles by femtosecond laser fragmentation in water

We report a size-controllable synthesis of stable aqueous solutions of ultrapure low-size-dispersed Au nanoparticles by methods of femtosecond laser fragmentation from preliminary formed colloids. Such approach makes possible the tuning of mean nanoparticle size between a few nm and several tens of nm under the size dispersion lower than 70% by varying the fluence of pumping radiation during the fragmentation procedure. The efficient size control is explained by 3D geometry of laser fragmentation by femtosecond laser-induced white light super-continuum and plasma-related phenomena. Despite the absence of any protective ligands, the nanoparticle solutions demonstrate exceptional stability due to electric repulsion effect associated with strong negative charging of formed nanoparticles. Stable aqueous solutions of bare gold nanoparticles present a unique object with a variety of potential applications in catalysis, surface-enhanced Raman spectroscopy, photovoltaics, biosensing and biomedicine.
In vitro propagation of Solidago virgaurea L . through nodal culture

A reliable in vitro propagation protocol has been established from nodal segments of a highly valuable medicinal plant Solidago virgaurea L. The explants were cultured on Murashige and Skoog’s medium augmented with different concentrations and combinations of plant growth regulators for shoot bud initiation and multiplications. Highest frequency of shoot proliferation (91.8 ± 0.64) and maximum number (12.1 ± 0.20) per node was observed in Murashige and Skoog’s medium augmented with4.5 mg/l of Kinetin in combination with 0.5 mg/l of Indole -3Acetic acid. Highest frequency (91.7 ± 1.43) of rooting and maximum number (3.8 ± 0.28) of rootlet per shoot let was achieved on Murashige and Skoog’s medium fortified with 4.5 mg/l of Indole -3Acetic acid in combination with 0.5 mg/l of Benzyl -6amino purine. Regenerated plants were successfully transferred to field (78%).
Second‐line Helicobacter pylori Eradication: A Randomized Comparison of 1‐week or 2‐week Bismuth‐containing Quadruple Therapy

Objectives: The increasing levels of bacterial antibiotic resistance have increased the need to evaluate the second‐line treatments for Helicobacter pylori. Bismuth‐based quadruple therapy is recommended as a second‐line treatment, but the optimal duration of this treatment is still debatable. We prospectively analyzed the eradication rate of H. pylori according to the duration of the second‐line bismuth‐based quadruple therapy.
Quantum algorithms: entanglement–enhanced information processing

We discuss the fundamental role of entanglement as the essential nonclassical feature providing the computational speedup in the known quantum algorithms. We review the construction of the Fourier transform on an Abelian group and the principles underlying the fast Fourier transform algorithm. We describe the implementation of the FFT algorithm for the group of integers modulo 2n in the quantum context, showing how the group–theoretic formalism leads to the standard quantum network and identifying the property of entanglement that gives rise to the exponential speedup (compared to the classical FFT). Finally we outline the use of the Fourier transform in extracting periodicities, which underlies its utility in the known quantum algorithms.
Pattern Completion in Symmetric Threshold-Linear Networks

Threshold-linear networks are a common class of firing rate models that describe recurrent interactions among neurons. Unlike their linear counterparts, these networks generically possess multiple stable fixed points (steady states), making them viable candidates for memory encoding and retrieval. In this work, we characterize stable fixed points of general threshold-linear networks with constant external drive and discover constraints on the coexistence of fixed points involving different subsets of active neurons. In the case of symmetric networks, we prove the following antichain property: if a set of neurons is the support of a stable fixed point, then no proper subset or superset of can support a stable fixed point. Symmetric threshold-linear networks thus appear to be well suited for pattern completion, since the dynamics are guaranteed not to get stuck in a subset or superset of a stored pattern. We also show that for any graph G, we can construct a network whose stable fixed points correspond precisely to the maximal cliques of G. As an application, we design network decoders for place field codes and demonstrate their efficacy for error correction and pattern completion. The proofs of our main results build on the theory of permitted sets in threshold-linear networks, including recently developed connections to classical distance geometry.
Reducing Energy Consumption of Disk Storage Using Power-Aware Cache Management

Reducing energy consumption is an important issue for data centers. Among the various components of a data center, storage is one of the biggest consumers of energy. Previous studies have shown that the average idle period for a server disk in a data center is very small compared to the time taken to spin down and spin up. This significantly limits the effectiveness of disk power management schemes. This paper proposes several power-aware storage cache management algorithms that provide more opportunities for the underlying disk power management schemes to save energy. More specifically, we present an off-line power-aware greedy algorithm that is more energy-efficient than Belady’s off-line algorithm (which minimizes cache misses only). We also propose an online power-aware cache replacement algorithm. Our trace-driven simulations show that, compared to LRU, our algorithm saves 16% more disk energy and provides 50% better average response time for OLTP I/O workloads. We have also investigated the effects of four storage cache write policies on disk energy consumption.