Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and sequence analysis of human and bovine corneal antigen (CO-Ag) cDNA: identification of host-parasite protein calgranulin C.

PURPOSE The primary structure of a cornea-associated antigen (CO-Ag) has been identified and has been implicated in the pathogenesis of Mooren's ulcer. The study designs were to isolate full-length clones encoding CO-Ag from a bovine and a human corneal cDNA library so that complete sequence analyses might further define the possible role of this protein in Mooren's ulcer. METHODS DNA fragments of bovine and human CO-Ag were generated using unique oligonucleotide primers and reverse transcription polymerase chain reaction. These fragments were used as probes to obtain cDNA clones from a bovine and a human corneal cDNA libraries. The clones with the longest cDNA inserts were selected for sequence analyses. Human cDNA fragment was digested with Stu I and Hind III and cloned into a expression vector, pPROEXHT, at the same restriction enzyme sites. The plasmid was transformed into E. coli cells. Correct cloning and the full-length sequence of human CO-Ag were determined by sequencing the insert cDNA. RESULTS The bovine cDNA insert sequence was 273 nucleotides in length for the entire mRNA coding region, 212 nucleotides in the 5' untranslated region, 83 nucleotides in the 3' untranslated region and a poly(A) tail. The DNA base sequence of this clone also contained a standard initiation codon, termination codon, and the polyadenylation signal. This cDNA predicts a protein which contains 91 amino acids with a molecular weight of 10,584 daltons. Plasmid expression vector, pPROEXHT-CO-Ag, was constructed that direct the synthesis of human CO-Ag in E. coli as fusion protein. Human CO-Ag fusion protein was purified to 90% pure with a yield of 17.2 mg per liter of the bacterial cell lysate. The nucleotide sequence of the CO-Ag cDNA insert was completely identical to human neutrophil calgranulin C. The deduced amino acid sequence was completely identical to a Ca(2+)-binding protein isolated on the surface of filarial nematodes. CONCLUSIONS The isolation and analysis of cDNA clones containing the complete coding sequence of bovine and human CO-Ag proteins is reported. The proteins identified by deduced amino acid sequences demonstrate 100% sequence homology with human and bovine calgranulin C. Immune recognition of calgranulin C to a filarial nematode may lead to a hyperactive autoimmune response to CO-Ag in the cornea leading to a Mooren's ulcer.
Inferring Robot Task Plans from Human Team Meetings: A Generative Modeling Approach with Logic-Based Prior

We aim to reduce the burden of programming and deploying autonomous systems to work in concert with people in time-critical domains, such as military field operations and disaster response. Deployment plans for these operations are frequently negotiated on-the-fly by teams of human planners. A human operator then translates the agreed upon plan into machine instructions for the robots. We present an algorithm that reduces this translation burden by inferring the final plan from a processed form of the human team's planning conversation. Our approach combines probabilistic generative modeling with logical plan validation used to compute a highly structured prior over possible plans. This hybrid approach enables us to overcome the challenge of performing inference over the large solution space with only a small amount of noisy data from the team planning session. We validate the algorithm through human subject experimentation and show we are able to infer a human team's final plan with 83% accuracy on average. We also describe a robot demonstration in which two people plan and execute a first-response collaborative task with a PR2 robot. To the best of our knowledge, this is the first work that integrates a logical planning technique within a generative model to perform plan inference.
Functional in situ assessment of muscle contraction in wild‐type and mdx mice

Introduction: Reports of muscle testing are frequently limited to maximal force alone. The experiments reported here show that force generation and relaxation rates can be obtained from the same experiments and provide a more complete functional characterization. Methods: Partial in situ testing was performed on the tibialis anterior of young wild‐type (WT) mice, young mdx mice, and old mdx mice. Force, force generation rate, and relaxation rates were measured during a fatigue test, 2 frequency–force tests, and a passive tension test. Results: We measured increased force but decreased force generation rate in WT compared with mdx muscles, and increased force but decreased relaxation rate of old compared with young mdx muscles. Young mdx muscles were the most sensitive to increases in passive tension. Conclusions: These measurements offer an improved understanding of muscle capability and are readily acquired by further analysis of the same tests used to obtain force measurements. Muscle Nerve 53: 260–268, 2016
Evaluating software specifications by comparison

It is a common practice in software development and other engineering domains to design more than one solution for a complex problem and consider only the most appropriate one. Similar practice is observed when procuring a new software product. The literature recommends this practice and intensively reveals a number of practical cases, yet is largely silent on how to make such a selection. In requirements engineering, an important issue is to provide a basis for judging and selecting one specification above others. This paper proposes through a case study, an approach to evaluate and compare two Object-Z specifications of the same set of requirements and hence, provides a means to select the most appropriate one. The approach recommends identifying properties expected from a satisfactory specification, uses existing validation techniques to evaluate proposed specifications and defines guidelines for comparison to facilitate the choice.
Neutrophil priming and activation in the pathogenesis of postinjury multiple organ failure.

The continuing study of multiple organ failure (MOF) has led to the development of inflammatory models of tissue injury in contrast to earlier infectious models. This change of focus is in response to more recent clinical observations suggesting that postinjury MOF frequently occurs in the absence of infection. In the alternative "two-hit" inflammatory model that has been proposed, the initial traumatic insult "primes" the inflammatory response such that a delayed, otherwise innocuous, inflammatory insult triggers an exaggerated response. The neutrophil (PMN), being uniquely equipped to cause oxidative tissue injury via the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase system, has been implicated as an early pivotal player in this model of postinjury MOF. Similar to the "two-hit" inflammatory model, circulating PMNs respond to proinflammatory mediators by becoming primed for enhanced superoxide anion (O2.) production and by increasing adherence to endothelium of organs that are susceptible to PMN-mediated injury. Subsequent proinflammatory insults promote further neutrophil sequestration and activate them for enhanced release of O2. -. The resulting tissue injury can be perpetuated and lead to eventual end-organ damage and failure. In terms of the NADPH oxidase system, PMN priming and activation by various agonists have been well documented in vitro and lead to increased endothelial damage. PMN priming and activation are also operable in an in vivo model of gut ischemia/reperfusion, a surrogate of shock and trauma resuscitation, leading to distant organ damage. Finally, in clinical studies of severely injured trauma patients, PMN priming and activation sequences identify patients at risk for developing MOF with its associated high mortality. Further characterization of the mechanisms that regulate PMN priming and activation in the trauma patient is necessary for the development of new therapeutic interventions designed to block deleterious PMN responses which lead to MOF while not compromising beneficial PMN functions of host defense and tissue repair.
Evidence of clozapine's effectiveness in schizophrenia: a systematic review and meta-analysis of randomized trials.

OBJECTIVE The purpose of this study was to evaluate all available trial-based evidence on the effectiveness of clozapine in schizophrenia as compared with conventional neuroleptics. METHOD All randomized, controlled trials comparing clozapine with a conventional neuroleptic in which there was satisfactory concealment of patients' treatment allocation were located through electronic searches in all languages of several databases and through contacting authors of recent trials as well as the manufacturer of clozapine. At least two independent reviewers assessed trials for inclusion in the study and extracted data for meta-analysis. RESULTS The review included 2,530 randomly assigned participants in 30 trials, most of them short-term. Clozapine-treated patients showed more clinical improvement and experienced significantly fewer relapses during treatment, although the risk of blood dyscrasias in long-term treatment may be as high as 7%. Scores on symptom rating scales showed greater improvement among clozapine-treated patients, who were also more satisfied with their treatment. However, there was no evidence that the superior clinical effect of clozapine is reflected in levels of functioning; on the other hand, global functional and pragmatic outcomes were frequently not reported. Clinical improvement was most pronounced in patients with treatment-resistant illness. CONCLUSIONS This meta-analysis confirms that clozapine is more effective than conventional neuroleptics in reducing symptoms of patients with both treatment-resistant and nonresistant schizophrenia. Future trials should be long-term pragmatic community trials or should address the effectiveness of clozapine in special patient populations. An international standard set of outcomes, including pragmatic assessments of functioning, would greatly enhance the comparison and summation of trials and future assessments of effectiveness.
Toxicity of Neem-Based Insecticides on Aquatic Animals and Cell Lines.

The impact o f pure azadirachtin (AZA) and neem-based insecticides (NeemixTM and Bioneem^^ on eight aquatic animals (crayfish, white shrimp, grass shrimp, blue crab, water fleas, oyster, freshwater snails, and mosquito) and two cells (hybridoma and oyster) were assessed by short term acute toxicity tests of 48 and 96 h. The LC50 {in vivo bioassays) and IC50 (in vitro bioassays) were determined for each species. Stability o f NeemixTM and BioneemTM was tested under light, air, and heat (24 and 37°C) for 1, 3, 6 , and 9 days. NeemixTM and BioneemTM were fractionated into two fractions (volatiles and nonvolatiies) and toxicities o f each were tested on water fleas. AZA showed less toxicity than NeemixTM and BioneemTM on all species tested. The toxic and molt inhibitory activity o f the insecticides were species, dose and time dependent. Among the test animals, water fleas was the most sensitive to NeemixTM, BioneemTM, and pure AZA with LC50 o f 0.071, 0.034, and 0.382 |ig AZA/mL, respectively. Next to water fleas, mosquito, oyster and blue crab were found to be very sensitive to NeemixTM and BioneemTM with low LC50 values. Crayfish and freshwater snails showed the least sensitivity to NeemixTM, BioneemTM and pure AZA. The LC50 values o f NeemixTM were 4.705 pg AZA/mL for crayfish and 4.257 pg AZA/mL for snails. NeemixTM and BioneemTM were foimd to be toxic to both hybridoma and oyster cells at concentration 1 pg AZA/mL and higher. The toxicity o f both insecticides
The role of natriuretic peptide administration in cardiovascular surgery-associated renal dysfunction: a systematic review and meta-analysis of randomized controlled trials.

OBJECTIVE Randomized controlled trials involving natriuretic peptide administration in the perioperative cardiovascular setting have shown inconsistent effects for renal and other clinical endpoints. The authors aimed to systematically review these trials to ascertain the role of natriuretic peptide administration in the management of cardiovascular surgery-associated renal dysfunction. DESIGN A systematic review and meta-analysis. SETTING A hospital. PARTICIPANTS A total of 934 adult patients from 13 randomized controlled trials. INTERVENTIONS Natriuretic peptides. MEASUREMENTS AND MAIN RESULTS MEDLINE, EMBASE, Cochrane Renal Health Library, and Google scholar were searched independently by 2 reviewers for randomized controlled studies comparing natriuretic peptides with placebo in patients undergoing cardiovascular surgeries. Studies reporting data on renal outcomes were included. Two reviewers independently assessed the studies for eligibility and extracted the relevant data. The pooled estimate showed that natriuretic peptide administration was associated with a reduction in acute renal failure requiring dialysis (odds ratio = 0.32 [0.15-0.66]) and a statistically nonsignificant trend toward a reduction in 30-day or in-hospital mortality (odds ratio = 0.59 [0.31-1.12]). Other benefits were a reduction in postsurgery peak serum creatinine levels, an increase in postsurgery urine output, a reduction in postsurgery serum aldosterone levels, and reductions in mechanical ventilation duration and intensive care unit stay length. Most of the included studies addressing this topic were small and lacked adequate power to reach statistical significance on their own. CONCLUSIONS Current literature analyzing studies evaluating the administration of natriuretic peptides in cardiovascular surgery may be associated with significant improvements in clinical outcomes. Given the limitations of meta-analysis, these observations need to be confirmed in a larger, adequately powered, prospective multicenter study.
An input current shaper using a Class-DE rectifier to meet IEC 61000-3-2 Class-C standard processing a small part of the total power

This paper proposed an electronic ballast that uses an input current shaper to reduce the total harmonic distortion of the line input current, that only process a small part of the total power. Base on the minimum value of the conduction angle to satisfy the requirements of the IEC 61000-3-2 Class-C standard, the conduction loss of the ICS stage can be reduced. The input current shaper is achieved by using a bridge rectifier which acts as the Class-DE resonant rectifier. By using this topology the conduction angle of the diode can be increased to high enough for satisfy the IEC 61000-3-2 Class-C standard requirements. The proposed electronic ballast is designed for 36-W fluorescent lamp and operated at a line rms voltage of 220 V, a line frequency of 50 Hz with the switching frequency fixed at about 76 kHz. The experimental results show that the total harmonic distortion is 29.5%, the power factor is 0.96, a lamp-current crest factor is 1.42, and 95.2% efficiency at full power.
Apoptosis of motor neurons with induction of caspases in the spinal cord after ischemia.

BACKGROUND AND PURPOSE Some neuronal subpopulations are especially vulnerable to ischemic injury. In the spinal cord, large motor neurons are vulnerable to ischemia and are selectively lost after transient ischemia. However, the mechanisms of the neuronal loss have been uncertain. We hypothesized that spinal motor neurons might be lost by apoptosis and investigated a possible mechanism of neuronal death by detection of double-strand breaks in genomic DNA and immunohistochemical analysis for caspases, ie, interleukin-1beta converting enzyme (ICE), Nedd-2, and CPP32. METHODS We used a rabbit spinal cord ischemia model created with a balloon catheter. The spinal cord was removed at 8 hours, 1, 2, or 7 days after 15 minutes of transient ischemia, and histological changes were studied with hematoxylin-eosin staining. To detect double-strand breaks in DNA, a staining with terminal deoxynucleotidyl transferase-mediated dUTP-biotin in situ nick end labeling (TUNEL) was performed. Furthermore, expression of ICE, Nedd-2, and CPP32 was investigated by Western blotting and immunohistochemical analysis. RESULTS Motor neurons were selectively lost at 7 days after transient ischemia. TUNEL study demonstrated that no cells were positively labeled until 1 day after ischemia, but nuclei of some motor neurons were positively labeled at 2 days. Western blot analysis revealed no immunoreactivity for ICE and slight immunoreactivities for Nedd-2 and CPP32 in the sham-operated spinal cords. However, immunoreactivity became apparent at 8 hours after transient ischemia, decreased at 1 day, and returned to baseline level at 2 days. Immunohistochemical analysis demonstrated that motor neurons were responsible for induction of those caspases. CONCLUSIONS Double-strand breaks in genomic DNA and induction of three caspases were demonstrated. These results indicate that motor neuron death in the spinal cord after transient ischemia is profoundly associated with activation of apoptotic processes.
Hubble Space Telescope ACS Weak-Lensing Analysis of the Galaxy Cluster RDCS 1252.9–2927 at z = 1.24

We present a weak-lensing analysis of one of the most distant massive galaxy clusters known, RDCS 1252.9-2927, at z = 1.24, using deep images from the Advanced Camera for Surveys (ACS) on board the Hubble Space Telescope (HST). By taking advantage of the depth and angular resolution of the ACS images, we detect for the first time at z > 1 a clear weak-lensing signal in both the i (F775W) and z (F850LP) filters. We measure a 5 σ signal in the i band and a 3 σ signal in the shallower z-band image. The two radial mass profiles are found to be in very good agreement with each other, and they provide a measurement of the total mass of the cluster inside a 1 Mpc radius of M(< 1 Mpc) = (8.0 ± 1.3) × 1014 M☉ in the current cosmological concordance model, h = 0.70, Ωm = 0.3, and ΩΛ = 0.7, assuming a redshift distribution of background galaxies as inferred from the Hubble Deep Field surveys. A weak-lensing signal is detected out to the boundary of our field (3' radius, corresponding to 1.5 Mpc at the cluster redshift). We detect a small offset between the centroid of the weak-lensing mass map and the brightest cluster galaxy, and we discuss the possible origin of this discrepancy. The cumulative weak-lensing radial mass profile is found to be in good agreement with the X-ray mass estimate based on Chandra and XMM-Newton observations, at least out to R500 ≃ 0.5 Mpc.
Tovel: Distributed Graph Clustering for Word Sense Disambiguation

Word sense disambiguation is a fundamental problem in natural language processing (NLP). In this problem, a large corpus of documents contains mentions to well-known (non-ambiguous) words, together with mentions to ambiguous ones. The goal is to compute a clustering of the corpus, such that documents that refer to the same meaning appear in the same cluster, subsequentially, each cluster is assigned to a different semantic meaning. In this paper, we propose a mechanism for word sense disambiguation based on distributed graph clustering that is incremental in nature and can scale to big data. A novel, heuristic vertex-centric algorithm based on the metaphor of the water cycle is used to cluster the graph. Our approach is evaluated on real datasets in both centralized and decentralized environments.
Heterogeneous multi-core platform for consumer multimedia applications

This paper presents a multi-core SoC architecture for consumer multimedia applications. The comprehensive functionality of such multimedia systems is described using the example of a hybrid TV application. The successful usage of a heterogeneous multi-core SoC platform is presented and it is shown how specific challenges such as inter-processor communication and real-time performance guarantees in physically centralized memory systems are addressed.
On the frequency domain accuracy of closed loop estimates

It has been argued that the frequency domain accuracy of high model-order estimates obtained on the basis of closed loop data is largely invariant to whether direct or indirect approaches are used. This paper revisits this study in light of new variance quantification results that apply for low model order and establishes that, under certain assumptions, there can be significant differences in the accuracy of frequency-response estimates that are dependent on what type of direct, indirect or joint input-output identification strategy is pursued.
Non-Traditional Security Issues and the Stability of Southeast Asia

Perubahan paradigma politik internasional berargumen bahwa diskursus keamanan non-tradisional (non-traditional security-NTS) adalah ancaman bagi keamanan. Pergeseran ini telah menarik minat para sarjana maupun pengambil kebijakan, seiring meningkatnya gejolak maupun dampak penting diskursus NTS terhadap keamanan pada tingkat domestik, regional, dan global. Diskursus NTS menyangkut perubahan iklim, bencana alam, migrasi, dan persoalan lintas batas yang melibatkan aktor non-negara dan berdampak pada negara dan masyarakat. Tulisan ini mengelaborasi tiga persoalan diskursus NTS, yaitu terorisme, peredaran obat terlarang, dan penyelundupan senjata ringan yang mengganggu stabilitas Asia Tenggara. Tulisan ini berargumentasi bahwa dari segi topografi, wilayah geografis yang bersifat terbuka, dan posisinya yang strategis menjadikan wilayah ini rentan terhadap ancaman. Konflik pada tingkat domestik yang terjadi di Kamboja, Vietnam, Filipina (Mindanao), Indonesia (Aceh) dan Thailand (Pattani) telah memberi ruang gerak bagi tindak kejahatan lintas batas ini. Tulisan ini terbagi menjadi empat bagian; pertama, tulisan ini mengungkap latar belakang konsep kemanan non-tradisional. Bagian selanjutnya berfokus pada bagaimana terorisme, peredaran obat terlarang dan penyelundupan senjata api ringan memengaruhi stabilitas Asia Tenggara secara keseluruhan. Berdasarkan data primer seperti dokumen resmi, laporan media terkait diskursus ini, tulisan ini menyimpulkan bahwa wilayah ini akan menjadi tempat berlangsungnya aktivitas keamanan non-tradisional jika hal ini terus dibiarkan. Harapannya, diskusi tulisan ini akan memerkaya diskursus dalam kajian hubungan internasional dan kajian kemanan regional, khususnya mengenai diskursus keamanan non-tradisional dan bisa menjadi referensi bagi para sarjana, mahasiswa hubungan internasional dan para pengambil keputusan. Kata kunci: keamanan non-tradisional, peredaran obat terlarang, penyelundupan senjata ringan, Asia Tenggara, terorisme