Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of 3'-end sequences in infectivity of poliovirus transcripts made in vitro

It has been shown by van der Werf et al. (S. van der Werf, J. Bradley, E. Wimmer, F. W. Studier, and J. Dunn, Proc. Natl. Acad. Sci. USA 83:2330-2334, 1986) that in vitro synthesis of poliovirus RNA by T7 RNA polymerase gives rise to infectious RNA molecules; however, these molecules are only 5% as infectious as RNA isolated from virions. A plasmid, T7D-polio, was constructed that allows the in vitro synthesis of full-length RNA molecules with two additional guanine residues at the 5' end. However, T7D-polio differed from the construct of van der Werf et al. in that RNA transcribed from T7D-polio has an authentic 3' end, ending with only a polyadenine nucleotide sequence. Transfection of these RNA molecules into mammalian cells produced wild-type poliovirus with an efficiency similar to that of virion RNA. The use of this vector in the characterization of viral mutants in vivo and in vitro is discussed.
Prevalence of Intestinal Parasitic Infections among School Children of Dadeldhura District, Nepal

Intestinal parasitic infestations are a common finding in the developing world, however, the patterns of parasitic distribution and rates are different elsewhere. The prevalence of intestinal parasitic infestation and chemical analysis of stool sample of the school children of age group 4-12 years in Dadeldhura district, far western region of Nepal. Out of 530 stool samples, 165 (31.13%) were found to be intestinal parasites positive. Among the total parasites, Hymenolepsis nana (46.56%) and Giardia lamblia (7.47%) were found in high prevalence as helmiths and protozoa respectively. Among the total stool samples 159 (30%) showed positive occult blood test. The prevalence of parasitic infection was found high in the children of age group 4-6 years (38.18%) than others though the result was not significant statistically (P>0.05). Highest prevalence of parasites was found in those not following the hygienic conditions (36.17%) than those following (18.83%). Similarly, high proportion of the parasites were found in children having gastrointestinal symptoms (49.23%) than in children without the gastrointestinal symptoms (13.70%) though the result was not significant statistically (P>0.05). The study showed the children using the water directly from the source had higher prevalence of parasites (32.13%) than those using treated water (14.28%). This study presents the high prevalence of stool parasites in school going children of Dadeldhura district.
On the coherence of ground motion in the San Fernando Valley

We present an analysis of the coherence of seismic ground motion recorded on alluvial sediments in the San Fernando Valley, California. Using aftershocks of the 17 January 1994 Mw6.7 earthquake recorded at a quasi-dense array of portable stations, we analyze the coherence of three well-recorded magnitude 3.7 to 4.0 events over the frequency range 0.5 to 15 Hz and a distance range of 0.5 to 5.3 km. All stations are located at sites with broadly similar near-site geology, characterized by medium to fine-grain Quaternary alluvial sediments. On average, relatively high values of coherence are observed for distances up to 3 to 4 km and frequencies up to 2 to 3 Hz; coherence drops sharply at frequencies near and above 3 Hz. Although average coherence functions are described reasonably well by a log-linear relationship with frequency, the curves at all distances exhibit a flattening at low frequencies that is not consistent with previous observations of coherence at hardrock sites. The distance decay of coherence is also markedly less strong, with high coherence values observed over station separations corresponding to multiple wavelengths. This may reflect fundamental differences in shallow-wave propagation in the two environments, with high-frequency scattering relatively more dominant in regions of hard-rock near-surface geology. Within a sedimentary basin or valley, the site response itself generally reflects a resonance phenomenon that may tend to give rise to more uniform ground motions. However, previous studies have demonstrated the existence of pathological focusing and amplification effects within complex sedimentary basin environments such as the greater Los Angeles region; our results undoubtedly do not quantify the full range of ground-motion variability at all sites, but rather represent the level of that variability that can be expected, and quantified, for typical source/receiver paths.
Insights into immunoglobulin E receptor signaling from structurally defined ligands

Summary: The asymmetrical structure of bent immunoglobulin E (IgE) bound to its high‐affinity receptor, FcɛRI, suggests a possible role for this configuration in the regulation of signaling mediated by cross‐linking of FcɛRI on the surface of mast cells and basophils. Indeed, the presence of bound IgE strongly influences the capacity of cross‐linked FcɛRI dimers to trigger mast cell degranulation, implicating orientational constraints by bound IgE. Bivalent ligands that cross‐link by binding to bivalent IgE can form linear and cyclic chains of IgE/FcɛRI complexes, and these exhibit only limited capacity to stimulate downstream signaling and degranulation, whereas structurally analogous trivalent ligands, which can form branched networks of cross‐linked IgE/FcɛRI complexes, are more effective at cell activation. Long bivalent ligands with flexible spacers can form intramolecular cross‐links with IgE, and these stable 1:1 complexes are very potent inhibitors of mast cell degranulation stimulated by multivalent antigen. In contrast, trivalent ligands with rigid double‐stranded DNA spacers effectively stimulate degranulation responses in a length‐dependent manner, providing direct evidence for receptor transphosphorylation as a key step in the mechanism of signaling by FcɛRI. Thus, studies with chemically defined oligovalent ligands show important features of IgE receptor cross‐linking that regulate signaling, leading to mast cell activation.
Purification and Biochemical Characterization of a Highly Thermostable Bacteriocin Isolated from Brevibacillus brevis Strain GM100

A bacteriocin-producing (11,000 AU mL(-1)) strain was isolated from the rhizosphere of healthy Algerian plants Ononis angustissima Lam. , and identified as Brevibacillus brevis strain GM100. The bacteriocin, called Bac-GM100, was purified to homogeneity from the culture supernatant, and, based on MALDI-TOF/MS analysis, was a monomer protein with a molecular mass of 4375.66 Da. The 21 N-terminal residues of Bac-GM100 displayed 65% homology with thurincin H from Bacillus thuringiensis. Bac-GM100 was extremely heat-stable (20 min at 120 °C), and was stable within a pH range of 3-10. It proved sensitive to various proteases, which demonstrated its protein nature. It was also found to display a bactericidal mode of action against gram-negative (Salmonella enteric ATCC 43972, Pseudomonas aeruginosa ATCC 49189, and Agrobacterium tumefaciens C58) and gram-positive (Enterococcus faecalis ENSAIA 631 and Staphylococcus aureus ATCC 6538) bacteria, and a fungistatic mode of action against the pathogenic fungus Candida tropicalis R2 CIP 203.
Loop-mediated isothermal amplification for diagnosis of 18 World Organization for Animal Health (OIE) notifiable viral diseases of ruminants, swine and poultry

Abstract Loop-mediated isothermal amplification (LAMP) is a simple, powerful state-of-the-art gene amplification technique used for the rapid diagnosis and early detection of microbial diseases. Many LAMP assays have been developed and validated for important epizootic diseases of livestock. We review the LAMP assays that have been developed for the detection of 18 viruses deemed notifiable of ruminants, swine and poultry by the World Organization for Animal Health (OIE). LAMP provides a fast (the assay often takes less than an hour), low cost, highly sensitive, highly specific and less laborious alternative to detect infectious disease agents. The LAMP procedure can be completed under isothermal conditions so thermocyclers are not needed. The ease of use of the LAMP assay allows adaptability to field conditions and works well in developing countries with resource-limited laboratories. However, this technology is still underutilized in the field of veterinary diagnostics despite its huge capabilities.
Plasma Exchange and Immunoadsorption of Patients with Thoracic Organ Transplantation

Primary organ failure after transplantation (TX) remains a serious complication and leads to a high percentage of lethality. It is known, however, that the speed of rejection and tissue destruction depends on 3 main factors: antibody titer, the ability of the tissue to repair itself, and immunosuppressive measures. Especially with evidence for antibodies against human leukocyte antigen (HLA-ab), the immunological risk of persistent and acute episodes of rejection increases. The role of non-HLA-ab in rejection episodes is often underestimated and should be studied further. Antibody-mediated rejection (AMR) is still an unsolved problem in thoracic organ TX. An essential pillar of antihumoral therapy are the extracorporeal procedures like plasmapheresis (PP), therapeutic plasma exchange (TPE), and immunoadsorption (IA), because only they have the ability to remove preformed or de novo developed antibodies quickly and effectively. The quick removal of antibodies and other plasma factors through TPE or IA remains an effective and supportive method for treating AMR and allows the TX despite preformed antibodies. The pertinent literature does not disclose, however, how often and for how long treatment should be administered. It is known, that repeated treatment cycles with adequately processed plasma volume must be used to overcome redistribution of pathological antibodies. Based on our experience in heart transplant recipients with compromised graft function due to non-HLA-ab and HLA-ab, IA seems to be more effective.
Quantum computing and polynomial equations over the finite field Z2

What is the computational power of a quantum computer? We show that determining the output of a quantum computation is equivalent to counting the number of solutions to an easily computed set of polynomials defined over the finite field Z2. This connection allows simple proofs to be given for two known relationships between quantum and classical complexity classes, namely BQP ⊆ PP and BQP ⊆ PP.
Analysis of gender based differences in auditory evoked potentials among healthy elderly population

Background: Influence of gender on auditory evoked potentials is contentious. Although there are quite a few studies documenting the gender as an influencing factor on auditory evoked potentials in younger subjects, but there is a lack of similar studies among elderly population. The present study was conducted to find out the pattern of gender based differences in auditory evoked potentials among healthy elderly subjects. Materials and Methods: A cross-sectional study was conducted on age matched, healthy males (n = 35) and females (n = 34), aged 50-70 years. The measures included latencies of waves I-V and interpeak latencies (IPL) I-III, III-V and I-V separately for both ears. Data was analyzed statistically using Students unpaired t-test, using Statistical Package for Social Sciences software v13.0. Results: The values of all the latencies and IPL for both the ears were non-significantly higher (P > 0.05) in males as compared to females. These results may be attributed to the differences in head circumference between both the genders and to the changed hormonal milieu of sex hormones after menopause. Conclusions: Statistical insignificance of latencies among male and female elderly subjects excludes gender as an influencing factor on auditory evoked potentials in this age group.
Varsity athletes have lower 2D:4D ratios than other university students

Abstract The second to fourth digit ratio (2D:4D) is a sexually dimorphic trait with lower finger ratios considered more masculine. These digit ratios are believed to reflect the prenatal hormonal environment with higher exposure to androgens in utero leading to more masculine digit ratios. The 2D:4D ratio has been negatively correlated with many factors, including aggression, physical fitness, and athleticism. We compared 2D:4D finger ratios of (1) male and female varsity athletes (n = 99) versus male and female student non-athletes (n = 122), and (2) males (n = 104) versus females (n = 117). Our results confirmed that both male (mean ± sx : 0.97 ± 0.004) and female (0.98 ± 0.005) varsity athletes had significantly lower ratios than their non-varsity peers (males: 0.99 ± 0.004; females: 1.00 ± 0.006), and that male athletes had significantly lower 2D:4D ratios than female athletes. Overall, males had significantly lower 2D:4D ratios than females (0.98 ± 0.003 vs. 0.99 ± 0.004). A smaller 2D:4D ratio appears to be consistent with participation in varsity sports among both males and females.
A matter of collection and detection for intraoperative and noninvasive near-infrared fluorescence molecular imaging: to see or not to see?

PURPOSE Although fluorescence molecular imaging is rapidly evolving as a new combinational drug/device technology platform for molecularly guided surgery and noninvasive imaging, there remains no performance standards for efficient translation of "first-in-humans" fluorescent imaging agents using these devices. METHODS The authors employed a stable, solid phantom designed to exaggerate the confounding effects of tissue light scattering and to mimic low concentrations (nM-pM) of near-infrared fluorescent dyes expected clinically for molecular imaging in order to evaluate and compare the commonly used charge coupled device (CCD) camera systems employed in preclinical studies and in human investigational studies. RESULTS The results show that intensified CCD systems offer greater contrast with larger signal-to-noise ratios in comparison to their unintensified CCD systems operated at clinically reasonable, subsecond acquisition times. CONCLUSIONS Camera imaging performance could impact the success of future "first-in-humans" near-infrared fluorescence imaging agent studies.
Monitoring Rainfall Patterns in the Southern Amazon with PERSIANN-CDR Data: Long-Term Characteristics and Trends

Satellite-derived estimates of precipitation are essential to compensate for missing rainfall measurements in regions where the homogeneous and continuous monitoring of rainfall remains challenging due to low density rain gauge networks. The Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks—Climate Data Record (PERSIANN-CDR) is a relatively new product (released in 2013) but that contains data since 1983, thus enabling long-term rainfall analysis. In this work, we used three decades (1983–2014) of PERSIANN-CDR daily rainfall data to characterize precipitation patterns in the southern part of the Amazon basin, which has been drastically impacted in recent decades by anthropogenic activities that exacerbate the spatio-temporal variability of rainfall regimes. We computed metrics for the rainy season (onset date, demise date and duration) on a pixel-to-pixel basis for each year in the time series. We identified significant trends toward a shortening of the rainy season in the southern Amazon, mainly linked to earlier demise dates. This work thus contributes to monitoring possible signs of climate change in the region and to assessing uncertainties in rainfall trends and their potential impacts on human activities and natural ecosystems.
Phosphorylation by the DHIPK2 Protein Kinase Modulates the Corepressor Activity of Groucho*

Groucho function is essential for Drosophila development, acting as a corepressor for specific transcription factors that are downstream targets of various signaling pathways. Here we provide evidence that Groucho is phosphorylated by the DHIPK2 protein kinase. Phosphorylation modulates Groucho corepressor activity by attenuating its protein-protein interaction with a DNA-bound transcription factor. During eye development, DHIPK2 modifies Groucho activity, and eye phenotypes generated by overexpression of Groucho differ depending on its phosphorylation state. Moreover, analysis of nuclear extracts fractionated by column chromatography further shows that phospho-Groucho associates poorly with the corepressor complex, whereas the unphosphorylated form binds tightly. We propose that Groucho phosphorylation by DHIPK2 and its subsequent dissociation from the corepressor complex play a key role in relieving the transcriptional repression of target genes regulated by Groucho, thereby controlling cell fate determination during development.
Secretagogin is Expressed by Developing Neocortical GABAergic Neurons in Humans but not Mice and Increases Neurite Arbor Size and Complexity

The neocortex of primates, including humans, contains more abundant and diverse inhibitory neurons compared with rodents, but the molecular foundations of these observations are unknown. Through integrative gene coexpression analysis, we determined a consensus transcriptional profile of GABAergic neurons in mid-gestation human neocortex. By comparing this profile to genes expressed in GABAergic neurons purified from neonatal mouse neocortex, we identified conserved and distinct aspects of gene expression in these cells between the species. We show here that the calcium-binding protein secretagogin (SCGN) is robustly expressed by neocortical GABAergic neurons derived from caudal ganglionic eminences (CGE) and lateral ganglionic eminences during human but not mouse brain development. Through electrophysiological and morphometric analyses, we examined the effects of SCGN expression on GABAergic neuron function and form. Forced expression of SCGN in CGE-derived mouse GABAergic neurons significantly increased total neurite length and arbor complexity following transplantation into mouse neocortex, revealing a molecular pathway that contributes to morphological differences in these cells between rodents and primates.
Fatty acid composition of blood serum lipoproteins from normal and ketotic cows.

Abstract Fatty acid analyses of α- and β -lipoproteins of normal, subclinical, and clinical ketotic cows during the early part of lactation have been performed. Sufficient data were obtained to reveal a large degree of individual animal variation. Nevertheless, significant differences between normal and ketotic cows regarding the α-lipoproteins' composition were detected. The β -lipoproteins show distinct fatty acid compositional trends, but the amount of individual variation obviates statistical significance. The data were interpreted as indicating alteraions in lipoprotein structure and supported the postulation that a breakdown in lipid and protein transport may be a primary event in bovine ketosis.
Tissue sensing adaptive radar for breast cancer detection: preliminary experimental results

Microwave breast cancer detection records the differences in electrical properties between healthy and malignant tissue. Tissue sensing adaptive radar (TSAR) has been proposed as a method for early tumor detection. Reflections from the differences in electrical properties between healthy and diseased tissue (tumors) are time-shifted and summed to create images. In this paper, the TSAR second generation experimental system is presented. An antenna is tested and characterized, reflections are recorded and the image formation algorithms are tested. Finally, preliminary tumor detection with the experimental setup is evaluated.
Hydrodynamic stretching of single cells for large population mechanical phenotyping

Cell state is often assayed through measurement of biochemical and biophysical markers. Although biochemical markers have been widely used, intrinsic biophysical markers, such as the ability to mechanically deform under a load, are advantageous in that they do not require costly labeling or sample preparation. However, current techniques that assay cell mechanical properties have had limited adoption in clinical and cell biology research applications. Here, we demonstrate an automated microfluidic technology capable of probing single-cell deformability at approximately 2,000 cells/s. The method uses inertial focusing to uniformly deliver cells to a stretching extensional flow where cells are deformed at high strain rates, imaged with a high-speed camera, and computationally analyzed to extract quantitative parameters. This approach allows us to analyze cells at throughputs orders of magnitude faster than previously reported biophysical flow cytometers and single-cell mechanics tools, while creating easily observable larger strains and limiting user time commitment and bias through automation. Using this approach we rapidly assay the deformability of native populations of leukocytes and malignant cells in pleural effusions and accurately predict disease state in patients with cancer and immune activation with a sensitivity of 91% and a specificity of 86%. As a tool for biological research, we show the deformability we measure is an early biomarker for pluripotent stem cell differentiation and is likely linked to nuclear structural changes. Microfluidic deformability cytometry brings the statistical accuracy of traditional flow cytometric techniques to label-free biophysical biomarkers, enabling applications in clinical diagnostics, stem cell characterization, and single-cell biophysics.
Nicotine Dependence, Physical Activity, and Sedentary Behavior among Adult Smokers

Background: Research has previously demonstrated an inverse association between smoking status and physical activity; however, few studies have examined the association between nicotine dependence and physical activity or sedentary behavior. Aim: This study examined the association between nicotine dependence and accelerometer-determined physical activity and sedentary behavior. Materials and Methods: Data from the 2003-2006 National Health and Nutrition Examination Survey (NHANES) were used. A total of 851 adult (≥20 years) smokers wore an accelerometer for ≥4 days and completed the Fagerstrom Test for Nicotine Dependence scale. Regression models were used to examine the association between nicotine dependence and physical activity/sedentary behavior. Results: After adjusting for age, gender, race-ethnicity, poverty level, hypertension, emphysema, bronchitis, body mass index (BMI), cotinine, and accelerometer wear time, smokers 50 + years of age with greater nicotine dependence engaged in more sedentary behavior (β = 11.4, P = 0.02) and less light-intensity physical activity (β = −9.6, P = 0.03) and moderate-to-vigorous physical activity (MVPA; β = −0.14, P = 0.003) than their less nicotine dependent counterparts. Conclusion: Older adults who are more nicotine dependent engage in less physical activity (both MVPA and light-intensity) and more sedentary behavior than their less nicotine dependent counterparts.
Processing Motion: Using Code to Teach Newtonian Physics

Prior to instruction, students often possess a common-sense view of motion, which is inconsistent with Newtonian physics. Effective physics lessons therefore involve conceptual change. To provide a theoretical explanation for concepts and how they change, the triangulation model brings together key attributes of prototypes, exemplars, theories, Bayesian learning, ontological categories, and the causal model theory. The triangulation model provides a theoretical rationale for why coding is a viable method for physics instruction. As an experiment, thirty-two adolescent students participated in summer coding academies to learn how to design Newtonian simulations. Conceptual and attitudinal data was collected using the Force Concept Inventory and the Colorado Learning Attitudes about Science Survey. Results suggest that coding is an effective means for teaching Newtonian physics.