Miracle-dz/UniFAR-FTUs huggingface dataset:
A highly efficient nonchemical method for isolating live nematodes (Caenorhabditis elegans) from soil during toxicity assays

The success of soil toxicity tests using Caenorhabditis elegans may depend in large part on recovering the organisms from the soil. However, it can be difficult to learn the International Organization for Standardization/ASTM International recovery process that uses the colloidal silica flotation method. The present study determined that a soil‐agar isolation method provides a highly efficient and less technically demanding alternative to the colloidal silica flotation method. Test soil containing C. elegans was arranged on an agar plate in a donut shape, a linear shape, or a C curve; and microbial food was placed outside the soil to encourage the nematodes to leave the soil. The effects of ventilation and the presence of food on nematode recovery were tested to determine the optimal conditions for recovery. A linear arrangement of soil on an agar plate that was sprinkled with microbial food produced nearly 83% and 90% recovery of live nematodes over a 3‐h and a 24‐h period, respectively, without subjecting the nematodes to chemical stress. The method was tested using copper (II) chloride dihydrate, and the resulting recovery rate was comparable to that obtained using colloidal silica flotation. The soil‐agar isolation method portrayed in the present study enables live nematodes to be isolated with minimal additional physicochemical stress, making it a valuable option for use in subsequent sublethal tests where live nematodes are required. Environ Toxicol Chem 2015;34:208–213. © 2014 SETAC
Penegakan Hukum Administrasi Dalam Pengelolaan Lingkungan Hidum

Adalah suatu hal yang jamak, bila trend globalisasi senantiasa diikuti oleh semakin tingginya akumulasi problem-problem lingkungan hidup dengan akselerasi yang jauh di atas penuntasan masalahnyq (termasuk dari aspek yuridis). Ini bisa dipahami,' . mengingat; penegakan hukum dalam hal ini memang, selain sulit, juga dilematis.
Requirement for the Rac GTPase in Chlamydia trachomatis Invasion of Non‐phagocytic Cells

Chlamydiae are gram‐negative obligate intracellular pathogens to which access to an intracellular environment is paramount to their survival and replication. To this end, chlamydiae have evolved extremely efficient means of invading nonphagocytic cells. To elucidate the host cell machinery utilized by Chlamydia trachomatis in invasion, we examined the roles of the Rho GTPase family members in the internalization of chlamydial elementary bodies. Upon binding of elementary bodies on the cell surface, actin is rapidly recruited to the sites of internalization. Members of the Rho GTPase family are frequently involved in localized recruitment of actin. Clostridial Toxin B, which is a known enzymatic inhibitor of Rac, Cdc42 and Rho GTPases, significantly reduced chlamydial invasion of HeLa cells. Expression of dominant negative constructs in HeLa cells revealed that chlamydial uptake was dependent on Rac, but not on Cdc42 or RhoA. Rac but not Cdc42 was found to be activated by chlamydial attachment. The effect of dominant negative Rac expression on chlamydial uptake is manifested through the inhibition of actin recruitment to the sites of chlamydial entry. Studies utilizing Green Fluorescent Protein fusion constructs of Rac, Cdc42 and RhoA, showed Rac to be the sole member of the Rho GTPase family recruited to the site of chlamydial entry.
A simple portable skin microscope for surface microscopy.

The search for a simple inexpensive portable microscope for surface examination of the skin continues. 1 In a number of large centers of dermatology, the large stereobinocular skin microscopes on fixed stands are used for special case studies in examination of patients and for research. However, for the busy clinic, or for office practice, unfortunately it is still necessary to use a simple portable microscope. Recently I have tried a microscope used by television technicians to examine single phosphor dots in the adjustment of the color-television tube. This is a cheap 8 in. microscope with magnification of × 25. The base is a clear plastic material which allows for the transmission of diffuse light at oblique angles to the surface of the skin. This plastic base can be cleansed very easily. The knurled knob on the side of the microscope allows for accurate focusing with the
Autoregulation of adenovirus E1A gene expression

We examined E1A gene expression by two evolutionarily divergent human adenoviruses, type 5 (subgroup C) and type 3 (subgroup B). Adenovirus type 3 (Ad3)-infected A549 cells contained much larger amounts of E1A-specific RNA than adenovirus type 5 (Ad5)-infected cells, from very early (3 h) through the late stages (20 h) after infection. The appearance of such abundant Ad3 E1A transcripts was delayed after infection of Ad5 E1A-expressing 293 cells, suggesting a down regulation of the Ad3 E1A gene by Ad5 E1A gene products. In a reciprocal manner, coinfection of A549 cells led to typically early and intense Ad3 E1A transcription and strongly inhibited transcription of the Ad5 E1A gene. Transient expression assays were developed so that the autoregulation of the E1A gene could be studied apart from the more complex background of infected cells. The DNA sequence surrounding the transcription start site of the Ad3 E1A gene was placed 5' to the sequence which encodes the bacterial chloramphenicol acetyltransferase gene. Cotransfection of HeLa cells with Ad3 or Ad5 E1A-expression plasmids increased the expression of the Ad3 E1A promoter-driven chloramphenicol acetyltransferase gene. Taken together, these results suggest dual autoregulatory features of adenovirus E1A gene expression. The positive and negative effects appear to be temporally distinguished under different conditions, both in viral infection and in transient assays with plasmid-cloned genes.
Self-organized criticality in a continuous, nonconservative cellular automaton modeling earthquakes.

We introduce a new nonconservative self-organized critical model. This model is equivalent to a quasistatic two-dimensional version of the Burridge-Knopoff spring-block model of earthquakes. Our model displays a robust power-law behavior. The exponent is not universal; rather it depends on the level of conservation. A dynamical phase transition from localized to nonlocalized behavior is seen as the level of conservation is increased. The model gives a good prediction of the Gutenberg-Richter law and an explanation to the variances in the observed {ital b} values.
Maximum Common Substructure-Based Data Fusion in Similarity Searching

Data fusion has been shown to work very well when applied to fingerprint-based similarity searching, yet little is known of its application to maximum common substructure (MCS)-based similarity searching. Two similarity search applications of the MCS will be focused on here. Typically, the number of bonds in the MCS, as well as the bonds in the two molecules being compared, are used in a similarity coefficient. The power of this technique can be extended using data fusion, where the MCS similarities of a set of reference molecules against one database molecule are fused. This "group fusion" technique forms the first application of the MCS in this work. The other application is that of the chemical hyperstructure. The hyperstructure concept is an alternative form of data fusion, being a hypothetical molecule that is constructed from the overlap of a set of existing molecules. This paper compares fingerprint group fusion (extended-connectivity fingerprints), MCS similarity group fusion, and hyperstructure similarity searching, and describes their relative merits and complementarity in virtual screening. It is concluded that the hyperstructure approach as implemented here is less generally effective than conventional fingerprint approaches.
Depletion of substance P and glutamate by capsaicin blocks respiratory rhythm in neonatal rat in vitro

The specific role of the neuromodulator substance P (SP) and its target, the neurokinin 1 receptor (NK1R), in the generation and regulation of respiratory activity is not known. The preBötzinger complex (preBötC), an essential site for respiratory rhythm generation, contains glutamatergic NK1R‐expressing neurones that are strongly modulated by exogenously applied SP or acute pharmacological blockade of NK1Rs. We investigated the effects of capsaicin, which depletes neuropeptides (including SP) and glutamate from presynaptic terminals, on respiratory motor output in medullary slice preparations of neonatal rat that generate respiratory‐related activity. Bath application of capsaicin slowed respiratory motor output in a dose‐ and time‐dependent manner. Respiratory rhythm could be restored by bath application of SP or glutamate transporter blockers. Capsaicin also evoked dose‐dependent glutamate release and depleted SP in fibres within the preBötC. Our results suggest that depletion of SP (or other peptides) and/or glutamate by capsaicin causes a cessation of respiratory rhythm in neonatal rat slices.
D3. Design and simulation of novel single-electron coding nano-circuits using room temperature summing-inverter gates

The Single-Electron (SE) summing-inverter (SI) NOR and NAND gates are among the basic functional SE circuits. In this paper, the design of multi-input SE SI NOR and NAND gates are reviewed. Novel SE decimal-to-BCD encoders and SE binary decoders, which are composed of SI gates, are designed for all combinations of active inputs and outputs. The simulated designs work properly with only one voltage source of 500 mV for a wide range of temperatures (from 40K to 400K). The detailed schematic diagrams along with the corresponding SIMON 2.0 simulation results at room temperature (that include input and output signals as well as the stability diagrams) of the novel SE decimal-to-BCD encoders as well as the developed SE binary decoders are presented.
Project Quality: The Achilles Heel of Offshore Technology Projects?

Technology projects today are being increasingly executed in project sourcing structures that span country boundaries. However, the performance implications of such offshoring efforts are often ambiguous vis-à-vis those that are executed within country boundaries. Further, little is known about project execution capabilities that may be central to improving the performance of offshore technology projects. This study attempts to shed light on the above issues using data from technology projects distributed within and across country boundaries. The study findings are twofold. First, a comparative analysis of project performance across 702 technology projects reveals that projects executed offshore realize significantly lower performance related to quality and technical goals compared with projects executed within country boundaries. Second, a subsequent in-depth analysis of the offshore technology projects in the sample highlights the enabling but differential performance effects of project execution capabilities. Specifically, we find that while risk management planning capability is central to improving project adherence to schedule and budgetary goals, agile project management capability is central to improving project adherence to quality and technical goals in technology projects executed offshore. The study concludes with a discussion of the findings, implications for technology research and practice, limitations, and directions for future research.
Effect of Self-Heating on the Drain Current Transient Response in AlGaN/GaN HEMTs

The self-heating effect on the drain current transient response in AlGaN/GaN high electron mobility transistors (HEMTs) was investigated experimentally. Two steps were observed as the drain current dropped with time. The relationship between the transient temperature rise in the channel and the drop in the drain current are discussed in detail. The decrease in the transient drain current and the rise in the channel transient temperature had a complementary relationship. The decrease in the channel electron mobility, caused by self-heating, was an important factor in the drain current drop in the AlGaN/GaN HEMTs.
Numerical Computation of Flame Spread over a Thin Solid in Forced Concurrent Flow with Gas-phase Radiation

Excerpts from a paper describing the numerical examination of concurrent-flow flame spread over a thin solid in purely forced flow with gas-phase radiation are presented. The computational model solves the two-dimensional, elliptic, steady, and laminar conservation equations for mass, momentum, energy, and chemical species. Gas-phase combustion is modeled via a one-step, second order finite rate Arrhenius reaction. Gas-phase radiation considering gray non-scattering medium is solved by a S-N discrete ordinates method. A simplified solid phase treatment assumes a zeroth order pyrolysis relation and includes radiative interaction between the surface and the gas phase.
Finding Bad Code Smells with Neural Network Models

Code smell refers to any symptom introduced in design or implementation phases in the source code of a program. Such a code smell can potentially cause deeper and serious problems during software maintenance. The existing approaches to detect bad smells use detection rules or standards using a combination of different object-oriented metrics. Although a variety of software detection tools have been developed, they still have limitations and constraints in their capabilities. In this paper, a code smell detection system is presented with the neural network model that delivers the relationship between bad smells and object-oriented metrics by taking a corpus of Java projects as experimental dataset. The most well-known object-oriented metrics are considered to identify the presence of bad smells. The code smell detection system uses the twenty Java projects which are shared by many users in the GitHub repositories. The dataset of these Java projects is partitioned into mutually exclusive training and test sets. The training dataset is used to learn the network model which will predict smelly classes in this study. The optimized network model will be chosen to be evaluated on the test dataset. The experimental results show when the model is highly trained with more dataset, the prediction outcomes are improved more and more. In addition, the accuracy of the model increases when it performs with higher epochs and many hidden layers.
Genetic analysis of human parainfluenza viruses circulating in Korea, 2006

Human parainfluenza viruses (HPIV) are important causes of respiratory tract infections in young children. To characterize the molecular epidemiology of an HPIV outbreak occurring in Korea during 2006, genetic analysis of 269 cell culture isolates from HPIV‐infected children, was conducted using nested reverse transcription‐PCR (RT‐PCR). HPIV‐1 was detected in 70.3% of tested samples (189/269). The detection rate of HPIV‐2 and HPIV‐3 was 1.5% (4/269) and 9.3% (25/269), respectively. Mixed HPIV‐1, ‐2 and ‐3 infections were detected in 19.0% (51/269): HPIV‐1 and HPIV‐2 in 15, HPIV‐1 and HPIV‐3 in 26, HPIV‐2 and HPIV‐3 in 6, and HPIV‐1, ‐2 and ‐3 in 4. Of these positive samples for three different types HIPV‐1, ‐2, and ‐3, two each representative strains were selected, the full length of hemagglutinin‐neuraminidase (HN) gene for HPIV was amplified by RT‐PCR, and sequenced. Multiple alignment analysis, based on reference sequence of HPIV‐1, ‐2, and ‐3 strains available in GenBank, showed that the identity of nucleotide and deduced amino acid sequences was 92.4–97.6% and 92.7–97.9%, respectively, for HPIV‐1, 88.5–99.8% and 88.6–100% for HPIV‐2, and 96.3–99.5% and 95.0–99.3% for HPIV‐3, respectively. Phylogenetic analysis showed that HPIV‐1, ‐2, and ‐3 strains identified in this study were closely related among the strains in the same type with no significant genetic variability. These results show that HPIV of multiple imported sources was circulating in Korea. J. Med. Virol. 86:1041–1047, 2014. © 2014 Wiley Periodicals, Inc.
Efficacy and safety of bevacizumab in metastatic colorectal cancer: pooled analysis from seven randomized controlled trials.

PURPOSE his analysis pooled individual patient data from randomized controlled trials (RCTs) to more thoroughly examine clinical outcomes when adding bevacizumab to chemotherapy for patients with metastatic colorectal cancer (mCRC). PATIENTS AND METHODS Patient data were pooled from the first-line AVF2107, NO16966, ARTIST, AVF0780, AVF2192, and AGITG MAX RCTs and the second-line E3200 RCT. All analyses were based on the intent-to-treat population. To assess differences in time-to-event variables by treatment (chemotherapy with or without placebo vs. chemotherapy plus bevacizumab), stratified random-effects (overall) and fixed-effects (subgroup comparisons) models were used to estimate pooled hazard ratios (HRs) and 95% confidence intervals (CIs). RESULTS The analysis population comprised 3,763 patients (1,773 chemotherapy with or without placebo; 1,990 chemotherapy plus bevacizumab). The addition of bevacizumab to chemotherapy was associated with statistically significant increases in overall survival (OS; HR, 0.80; 95% CI, 0.71-0.90) and progression-free survival (PFS; HR, 0.57; 95% CI, 0.46-0.71). The effects on OS and PFS across subgroups defined by chemotherapy backbone (oxaliplatin-based, irinotecan-based), extent of disease (liver metastases only, extensive disease), age (<65, ≥65 years), Eastern Cooperative Oncology Group performance status (0, ≥1), and KRAS status (wild-type, mutant) were consistent with the overall analysis. Incidence rates of grade ≥3 hypertension, proteinuria, bleeding, wound-healing complications, gastrointestinal perforations, and thromboembolic events were increased with bevacizumab treatment. CONCLUSION The use of bevacizumab with chemotherapy resulted in statistically significant increases in OS and PFS for patients with mCRC. The PFS benefit extended across the clinically relevant subgroups examined. The observed safety profile of bevacizumab was consistent with that reported in individual trials.
Killing of human myelomonocytic leukemia and lymphocytic cell lines by Actinobacillus actinomycetemcomitans leukotoxin

The purified leukotoxin of Actinobacillus actinomycetemcomitans kills human leukemic cell lines (e.g., HL-60, U937, and KG-1) and human T- and B-cell lines (e.g., JURKAT, MOLT-4, Daudi, and Raji) in a dose- and time-dependent manner. The 50% effective doses for these cell lines are similar to those established for human polymorphonuclear leukocytes and monocytes. In contrast, other human and nonhuman tumor cell lines are not susceptible to the leukotoxin. These human leukemia and lymphoid cell lines will serve as useful model systems with which to study the molecular specificity and mechanism(s) of action of the actinobacillus leukotoxin.
Non-autonomic component in bradycardia of endurance trained men at rest and during exercise.

Autonomic nervous alterations have generally been held responsible for the bradycardia of the endurance athlete. In order to determine whether there is also a non-autonomic component in the bradycardia of long-term training, we compared the intrinsic heart rate (HR) of highly trained bicyclists (heart volume: 995 +/- 155 ml) with that of untrained men (heart volume: 805 +/- 195 ml) at rest and during bicycle ergometer exercise at 50, 75 and 100% of maximal oxygen uptake (VO2 max.) Intrinsic HR was achieved by combined vagal and beta-adrenergic blockade with atropine and propranolol or metoprolol (cardioselective) injected intravenously. Intrinsic HR was significantly lower in trained (T) than in untrained (UT) at rest and at all levels of exercise. The chronotropic reserve from resting HR to maximal HR was identical in the two groups. Nearly identical intrinsic HRs were achieved with atropine and either beta-adrenergic antagonist. HR differences between T and UT were very similar in magnitude--approximately 13 beats/min--at rest and during exercise at a given percentage of VO2 max, with and without autonomic blockade. Evidence is thus provided for a non-autonomic component in the bradycardia of well-trained men which may be responsible for a parallel downward shift in the relationship between HR and percentage of VO2 max. The lower intrinsic HR in well-trained men might be explained by, i.a. the cardiac enlargement.
Invasion of Winter Moth in New England: Effects of Defoliation and Site Quality on Tree Mortality

Widespread and prolonged defoliation by the European winter moth, Operophtera brumata L. , has occurred in forests of eastern Massachusetts for more than a decade and populations of winter moth continue to invade new areas of New England. This study characterized the forests of eastern Massachusetts invaded by winter moth and related the duration of winter moth defoliation estimated using dendrochronology to observed levels of tree mortality and understory woody plant density. Quercus basal area mortality in mixed Quercus and mixed Quercus—Pinus strobus forests in eastern Massachusetts ranged from 0-30%; mortality of Quercus in these forests was related to site quality and the number of winter moth defoliation events. In addition, winter moth defoliation events lead to a subsequent increase in understory woody plant density. Our results indicate that winter moth defoliation has been an important disturbance in New England forests that may have lasting impacts.
Observability relations and observability don't cares

The observability relation O(x,z) or the Boolean relation provides a description of all the flexibility one has in implementing a Boolean network N. The authors represent and use this flexibility in a logic synthesis system by adding a single output node to the Boolean network N. The node function for the new node is O(x,z). The newly constructed network N' (called the observability network) has only one output and computes 1 for every input x. It is shown that the observability don't cares (ODCs) for a node y/sub i/ in N' provide the maximum flexibility for implementing y/sub i/ and subsume the flexibility obtained for y/sub i/ in N even with don't cares provided at each output. This gives rise to new methods for computing complete ODCs for N' and hence for N. <<ETX>>
Termination of System F-bounded: A Complete Proof

Abstract SystemF-bounded is a second-order typedλ-calculus with subtyping which has been defined to carry out foundational studies about the type systems of object-oriented languages. The almost recursive nature of the essential feature of this system makes one wonder whether it retains the strong normalization property, with respect to first- and second-orderβϵreduction of systemF⩽. We prove that this is the case. The proof is carried out to the last detail to allow the reader to be convinced of its correctness.
An error control scheme for transmission of vector quantization data over noisy channels

This paper presents an error control scheme for transmitting vector-quantized data over noisy channels. First, we review a self-organizing feature map (SOFM) based approach to construct the mapping from the codebook of the quantizer to the channel signal set of the communication system. This approach is robust with respect to channel noise even if we do not use any error control scheme in the communication system. Afterwards, a new trellis type quantizer, namely, the trellis coded Kohonen (1984) map (TCKM), is presented. The design process of the TCKM, which is based on the neighborhood structure of SOFMs, is simpler than that of conventional trellis coded vector quantizers (TCVQs). Simulation results show that the performance of TCKMs is comparable with that of TCVQs. Last, we introduce the error control scheme based on the concepts of the above two applications of SOFMs. Simulation results show that the proposed error control scheme is more robust with respect to channel noise. The advantage of our approaches mentioned above is that the design processes of transmission systems are predefined before the construction of the codebook. Thus, different codebooks with the same neighborhood structure can share the same design.