Miracle-dz/UniFAR-FTUs huggingface dataset:
Involvement of multiple genetic determinants in high-level methicillin resistance in Staphylococcus aureus

A methicillin-susceptible, novobiocin-resistant strain of Staphylococcus aureus (RN2677; methicillin MIC, 0.8 micrograms/ml) was transformed with DNA prepared from highly and homogeneously methicillin-resistant S. aureus strains (methicillin MIC, greater than or equal to 400 micrograms/ml) or from heterogeneous strains in which the majority of cells had a low level of resistance (methicillin MIC, 6.3 micrograms/ml). All methicillin-resistant transformants showed low and heterogeneous resistance (methicillin MIC, 3.1 micrograms/ml) irrespective of the resistance level of DNA donors. All transformants examined produced normal amounts of the low-affinity penicillin-binding protein (PBP) 2a, and methicillin resistance and the capacity to produce PBP 2a showed the same degree of genetic linkage to the novobiocin resistance marker with both homogeneous and heterogeneous DNA donors. Next, we isolated a methicillin-susceptible mutant from a highly and homogeneously resistant strain which had a Tn551 insertion near or within the PBP 2a gene and thus did not produce PBP 2a. With this mutant used as the recipient, genetic transformation of the methicillin resistance gene was repeated with DNA isolated either from highly and homogeneously resistant strains or from heterogeneous (low-resistance) strains. All transformants obtained expressed high and homogeneous resistance and produced PBP 2a irrespective of the resistance level of the DNA donors. Our findings suggest that (i) the methicillin resistance locus is identical to the structural gene for PBP 2a, (ii) although the ability to produce PBP 2a is essential for resistance, the MICs for the majority of cells are not related to the cellular concentration of PBP 2a, and (iii) high MICs and homogeneous expression of resistance require the products of other distinct genetic elements as well.
The construct of psychopathy in a Chilean prison population.

OBJECTIVE To test the four-factor model of the Hare Psychopathy Checklist - Revised (PCL-R) empirical construct of psychopathy in a Chilean prison population by using instruments that supply different types of data. METHODS Two hundred and nine male inmates of the Prison of Los Andes, Chile, were evaluated. Confirmatory factor analysis was carried out with the PCL-R and the Self-Report of Psychopathy - III - Short Form (SRP-III-SF). RESULTS The distributions of total PCL-R and SRP-III-SF scores were normal (Kolmorogov-Smirnov [K-S] = 1.04, p = 0.230; K-S = 0.812, p = 0.525, respectively), with means of 20.9 ± 6.8 for the former and 61.6 ± 15.2 for the latter. Model fit was good for the PCL-R (Tucker Lewis index [TLI] = 0.96; root mean square error of approximation [RMSEA] = 0.04) and for the SRP-SF (TLI = 0.94, RMSEA = 0.04). CONCLUSIONS The results obtained with the PCL-R and the SRP-SF showed adequate fit to the empirical four-factor model of psychopathy and support this model. As foreseeable, fit was better for the PCL-R, which combines several sources of information.
A Cre Mouse Line for Probing Irradiance- and Direction-Encoding Retinal Networks

Abstract Cell type-specific Cre driver lines have revolutionized the analysis of retinal cell types and circuits. We show that the transgenic mouse Rbp4-Cre selectively labels several retinal neuronal types relevant to the encoding of absolute light intensity (irradiance) and visual motion. In the ganglion cell layer (GCL), most marked cells are wide-field spiking polyaxonal amacrine cells (ACs) with sustained irradiance-encoding ON responses that persist during chemical synaptic blockade. Their arbors spread about 1 mm across the retina and are restricted to the inner half of the ON sublamina of the inner plexiform layer (IPL). There, they costratify with dendrites of M2 intrinsically photosensitive retinal ganglion cells (ipRGCs), to which they are tracer coupled. We propose that synaptically driven and intrinsic photocurrents of M2 cells pass through gap junctions to drive AC light responses. Also marked in this mouse are two types of RGCs. R-cells have a bistratified dendritic arbor, weak directional tuning, and irradiance-encoding ON responses. However, they also receive excitatory OFF input, revealed during ON-channel blockade. Serial blockface electron microscopic (SBEM) reconstruction confirms OFF bipolar input, and reveals that some OFF input derives from a novel type of OFF bipolar cell (BC). R-cells innervate specific layers of the dorsal lateral geniculate nucleus (dLGN) and superior colliculus (SC). The other marked RGC type (RDS) is bistratified, transient, and ON-OFF direction selective (DS). It apparently innervates the nucleus of the optic tract (NOT). The Rbp4-Cre mouse will be valuable for targeting these cell types for further study and for selectively manipulating them for circuit analysis.
Application of Omics and Bioinformatics Technologies in Response to COVID-19 Pandemic

The medical biotechnology community has undertaken significant endeavors to gain a comprehensive understanding of SARS-CoV-2’s biology and pathogenesis mechanisms. Omics approaches and technologies have been widely employed in the fight against SARS-CoV-2. Since the onset of the virus outbreak, researchers have demonstrated how recent omics and bioinformatics technological advancements have contributed to the diagnosis, vaccine development, treatment, and control of disease transmission. Studies conducted since the outbreak have been collected and summarized, with a focus on bioinformatics approaches and their contribution to controlling this pandemic. Developments and advanced omics technology in connection to the COVID-19 pandemic have been analyzed. The multi-omics technology, which offers various strategies in identifying potential diagnostics, therapeutics, studies of variants of concern, and drug repurposing approaches, has been assessed. Pandemic response has seen the application of multi-omics and pan-genomics approaches, including genomics, metabolomics, transcriptomics, proteomics, epigenomics, clustered regularly interspaced short palindromic repeats (CRISPR) technology, host-pathogen interactions, artificial intelligence, and machine learning in various research areas. Additionally, bioinformatics and mathematical modeling have played a significant role in disease control. The use of smart technologies to control virus transmission and predict patients’ health conditions and treatment outcomes has also been crucial. Transcriptome analysis has emerged as a major application, contributing to the generation of new knowledge on viral sequences and intracellular signaling pathways that regulate viral infection and pathogenesis mechanisms. The sequencing of the virus has paved the way for the use of omics technologies and an integrative technique in combating the pandemic. In general, the advancement of omics technology during this pandemic has been fascinating and has contributed a significant role to the science of health biotechnology in general and omics and bioinformatics in particular.Keywords: bioinformatics, coronavirus, COVID-19, omics, SARS COV-2
Wilms' tumor: An update

Wilms' tumor (WT) is the commonest pediatric renal tumor, predominantly seen in children less than five years of age. The majority of patients present with an abdominal lump and CT scan is the usual imaging modality for determining the extent of disease. With multimodality management, the results of treatment of WT have improved dramatically over the last 50 years. The treatment protocols have been devised and modified repeatedly depending on evidence from randomized trials by several cooperative groups - mainly National Wilms' Tumor Study Group (NWTSG) and the International Society of Pediatric Oncology (SIOP). The NWTSG recommends primary surgery followed by chemotherapy while SIOP advocates four weeks of chemotherapy prior to surgery. The regimen, dose and duration of chemotherapy have been repeatedly modified to reduce toxicity while maintaining efficacy. The role of radiation therapy has also been customized. Most centers have reported excellent survival rates with the modern day treatment protocols, except in patients with an unfavorable histology. The results of treatment of relapsed WT have also improved with newer drugs and combinations being used for the same.
Determining Beach User Knowledge of Rip Currents in Costa Rica

ABSTRACT Llopis, I.A. ; Echeverria, A.G. ; Trimble, S. ; Brannstrom, C. , and Houser, C. , 2018. Determining beach user knowledge of rip currents in Costa Rica. Rip currents account for over 50 drownings a year in Costa Rica, with most drownings involving young single male students at beaches in close proximity to San Jose. The hazard posed by a rip current in Costa Rica and elsewhere depends in part on beach user knowledge of the rip current hazard and their ability to identify the situations in which there is the potential for drowning or need for rescue. This study describes the results of beach user surveys (n = 171) completed in English and Spanish at Jacó Beach on the central Pacific coast and Cocles Beach on the Caribbean coast of Costa Rica in 2013 and 2014. Rip current knowledge amongst national (domestic) and foreign tourists was estimated on both beaches. Results suggest that the amount of time spent in the water, activities on the beach, and self-assessment of swimming abilities help to explain why more males drown despite similar populations of males and females at both beaches. The personal and group behaviors that increase the potential for drowning are exacerbated by problems with the rip current warning system used at each beach. Approximately 58% of respondents did not observe the warnings, and 41% self-reported not changing their behavior after observing the sign, with 40% of respondents noting that the messages on the signs were confusing. Results of the study highlight the need to design and employ more effective warning signs, to set up a national certified lifeguard corps, and to plan educational activities aimed at those who are at greatest risk to drowning. This assessment and the identified need to develop a national policy can serve as a model for other countries in Central America and elsewhere where rip current–related drownings are a public health concern.
Sun Protection Preferences and Behaviors among Young Adult Males during Maximum Ultraviolet Radiation Exposure Activities

This study explores sun protection attitudes, preferences, and behaviors among young adult males participating in an open-field activity with extreme ultraviolet radiation exposure. Male drum corps members (n = 137) responded to survey questions regarding their behavior and willingness to engage in sun protection and barriers to sunscreen usage. A subset of members (n = 31) participated in cognitive interviews exploring various sunscreen products and intervention techniques. Participants were knowledgeable about health risks and protection benefits regarding sun exposure. Generally, males had positive attitudes and normative beliefs about using sunscreen. A barrier to sunscreen re-application was lack of adequate time to reapply sunscreen during the open field activity. Males preferred a towelette application method, but were unfamiliar with its efficacy and proper use. Thus, they were more likely to use the more familiar sunscreen spray. To increase sun protection behaviors and lower skin cancer risk for males participating in open-field activities, breaks must be allotted every 2 h and have sufficient time to allow sunscreen application. Future development and research into delivery systems that rapidly and evenly apply sunscreen may help lower exposure in this population.
Mexiletine: Pharmacology and therapeutic use

Mexiletine is a Class IB antiarrhythmic which has basic and clinical electrophysiologic properties similar to lidocaine. Like other Class I antiarrhythmic agents, mexiletine blocks the rapid inward sodium current responsible for phase 0 of the action potential. It has been noted in the clinical electrophysiology laboratory to have minimal effect on sinus node function and AV nodal and His‐Purkinje system conduction. Pharmacokinetic studies have shown that oral absorption is rapid with bioavailability of 80‐90%. Mexiletine is predominantly metabolized by the liver with elimination half‐life of 9 to 12 hours. The antiarrhythmic effects of the primary drug's metabolites remain to be defined. Hemodynamic studies have shown mexiletine to have a lesser negative inotropic effect than procainamide or disopyramide. Although mexiletine as a single agent successfully suppresses 60 to 80% of spontaneous ventricular arrhythmias, it has lower efficacy in suppression of induced ventricular arrhythmias. Multiple studies have shown that as monotherapy mexiletine is effective in preventing the induction of ventricular tachycardia in approximately 20% of patients. When used in combination with a Class IA antiarrhythmic drug for suppression of induced ventricular arrhythmias, multiple investigators have reported greater efficacy. Neurological side effects (tremor, dizziness, memory loss) occur in approximately 10% of patients while gastrointestinal side effects (nausea, anorexia, gastric irritation) occur in up to 40% of patients. Proarrhythmia or other serious toxicity from the drug is uncommon.
Skeletal development in Xenopus laevis (Anura: Pipidae)

Postembryonic skeletal development of the pipid frog Xenopus laevis is described from cleared‐and‐stained whole‐mount specimens and sectioned material representing Nieuwkoop and Faber developmental Stages 46–65, plus postmetamorphic individuals up to 6 months old. An assessment of variation of skeletogenesis within a single population of larvae and comparison with earlier studies revealed that the timing, but not the sequence, of skeletal development in X. laevis is more variable than previously reported and poorly correlated with the development of external morphology. Examination of chondrocranial development indicates that the rostral cartilages of X. laevis are homologous with the suprarostral cartilages of non‐pipoid anurans, and suggests that the peculiar chondrocranium of this taxon is derived from a more generalized pattern typical of non‐pipoid frogs. Derived features of skeletal development not previously reported for X. laevis include (1) bipartite formation of the palatoquadrate; (2) precocious formation of the adult mandible; (3) origin of the angulosplenial from two centers of ossification; (4) complete erosion of the orbital cartilage during the later stages of metamorphosis; (5) development of the sphenethmoid as a membrane, rather than an endochondral bone; and (6) a pattern of timing of ossification that more closely coincides with that of the pelobatid frog Spea than that recorded for neobatrachian species. © 1992 Wiley‐Liss, Inc.
Study on Pantograph Arcing in a Laboratory Simulation System by High-Speed Photography

Phenomena of the pantograph arcing have become a challenge for the further development of high-speed electrified railway system. Despite of the large attention that has been paid to the radiated electromagnetic interference, materials ablation as well as the power-quality decline resulted from pantograph arcing, the specific dynamics of pantograph arcing with a high time resolution are still in absence. In this paper, the pantograph arcing phenomena in a laboratory simulation system were experimentally studied by high-speed photography. Synchronized electrical voltage and current waveforms were obtained to acquire a more comprehensive understanding on the underlying physics. The overall dynamics of the pantograph arcing from ignition to extinguishment were recorded. Three stages of the electriccontact process, from approaching arc, mechanical contact to the drawn arc, were well distinguished. A much intensified drawn arc was observed than the approaching arc. Typical lasting time of the drawn arcing is found ~4 times larger than the approaching arcing for our test setup. Maximum diameter of 3.3 mm was reached at around the current-peak moment. An interesting stable arc voltage of ~23 V was found during the drawn arcing. Intense material splash above the carbon strip was observed during the arcing process. The transient resistance during a typical arcing period was also analyzed, and a minimum value of ~100 mQ was determined.
Exposure to West Nile virus and tick‐borne encephalitis virus in dogs in Spain

In the past decade, the spread of emerging zoonotic flaviviruses (genus Flavivirus, family Flaviviridae) has been reported in many regions worldwide, representing a threat to both human and animal health. A serosurvey was carried out to assess exposure and risk factors associated with antigenically related flaviviruses, particularly West Nile virus (WNV), Usutu virus (USUV) and tick-borne encephalitis virus (TBEV), in dogs in Spain. Flavivirus antibodies were detected in 39 of 815 dogs (4.8%; 95% CI: 3.3-6.3) by bELISA. Significantly higher seropositivity was observed in hunting dogs compared to pet dogs. Virus neutralization tests confirmed WNV-specific and TBEV-specific antibodies in 11 and 14 bELISA-positive dogs, respectively. This is the first serosurvey of WNV and TBEV in dogs in Spain and the first report of TBEV circulation in this country. The seropositivity obtained indicates widespread, but not homogeneous, distribution of WNV and TBEV in dogs in Spain. In 2013 and 2015, WNV-seropositive dogs were detected in those areas of Andalusia where the highest number of WNV outbreaks were reported in both horses and humans. Antibodies against TBEV have been found in dogs sampled in two different periods and regions in Spain. Serosurveillance in dogs could be a complementary way of monitoring the activity of emerging flaviviruses in Spain.
Distribution of Putative Adhesins in Different Seropathotypes of Shiga Toxin-Producing Escherichia coli

ABSTRACT The distribution of eight putative adhesins that are not encoded in the locus for enterocyte effacement (LEE) in 139 Shiga toxin-producing Escherichia coli (STEC) of different serotypes was investigated by PCR. Five of the adhesins (Iha, Efa1, LPFO157/OI-141, LPFO157/OI-154, and LPFO113) are encoded in regions corresponding to genomic O islands of E. coli EDL933, while the other three adhesins have been reported to be encoded in the STEC megaplasmid of various serotypes (ToxB [O157:H7], Saa [O113:H21], and Sfp [O157:NM]). STEC strains were isolated from humans (n = 54), animals (n = 52), and food (n = 33). They were classified into five seropathotypes (A through E) based on the reported occurrence of STEC serotypes in human disease, in outbreaks, and in the hemolytic-uremic syndrome (M. A. Karmali, M. Mascarenhas, S. Shen, K. Ziebell, S. Johnson, R. Reid-Smith, J. Isaac-Renton, C. Clark, K. Rahn, and J. B. Kaper, J. Clin. Microbiol. 41:4930-4940, 2003). The most prevalent adhesin was that encoded by the iha gene (91%; 127 of 139 strains), which was distributed in all seropathotypes. toxB and efa1 were present mainly in strains of seropathotypes A and B, which were LEE positive. saa was present only in strains of seropathotypes C, D, and E, which were LEE negative. Two fimbrial genes, lpfAO157/OI-141 and lpfAO157/OI-154, were strongly associated with seropathotype A. The fimbrial gene lpfAO113 was present in all seropathotypes except for seropathotype A, while sfpA was not present in any of the strains studied. The distribution of STEC adhesins depends mainly on serotypes and not on the source of isolation. Seropathotype A, which is associated with severe disease and frequently is involved in outbreaks, possesses a unique adhesin profile which is not present in the other seropathotypes. The wide distribution of iha in STEC strains suggested that it could be a candidate for vaccine development.
Nature of the Ambient Noise, Site Response, and Orientation of Ocean?Bottom Seismometers (OBSs): Scientific Results of a Passive Seismic Experiment in the Andaman Sea

We analyze the nature of the ambient noise and site response for Ocean Bottom Seismometers (OBSs) deployed in the Andaman region. The probabilistic power spectral densities (PPSDs) of the OBSs show that the noise level in the Andaman region is within the range of Peterson’s new low noise model (NLNM) and new high noise model (NHNM) for short periods (< 20 s). For long periods (> 20 s), the noise level is higher than NHNM. The peak associated with secondary microseisms occurs between 3 and 6 s. The stations that are close to the Andaman and Nicobar Islands show a prominent secondary microseismic peak at 4 s while the stations farther away show a small hump at 1 s. The noise level varies seasonally and shows a strong correlation with the significant wave height (SWH) computed from WAVEWATCH III. The ambient noise is down to 140 dB for the band from 0.1 s to 1 s, which provides the best signal-to-noise level for local earthquakes. For very short periods (< 0.1 s), the ambient noise level increases to -120 dB probably due to the efficient propagation of seismic energy through the low attenuation oceanic crust. The horizontal-to-vertical spectral ratio (HVSR) of the ambient noise curves shows an amplification factor greater than four. Furthermore, the HVSR curves show a broad/flat peak beneath the seamounts and the accretionary prism and a sharp/clear peak in the basinal area. We also estimate the orientation of the OBSs using Rayleigh wave polarization analysis.
The Origin of Fine Sediment Determines the Observations of Suspended Sediment Fluxes Under Unsteady Flow Conditions

Field observations in a wide range of environments have shown that sediment availability is a major control on the suspended sediment observations in streams. Here we examine, via laboratory experiments, how the amount of proximal in‐channel fine sediment storage relative to the upstream fine sediment distal supply influences the observations of suspended sediment concentrations in streams. Experiments under idealized conditions in a laboratory flume with different ratios of proximal and distal sediment supplies were conducted under a varying flow regime. In addition, the role of the sediment particle size of the supplied sediment on suspended sediment observations was explored. The combinations of proximal and distal sediment supply result in multiple responses of the channel bed and sediment quantity within the channel bed, and the responses adjust through aggradation and degradation. The signature of sediment concentration observed at the upstream section of the channel, given by the distal supply, differs from the downstream observations of the total conveyed sediment (distal and proximal), as shown by an in‐phase analysis of sediment concentration‐discharge plots. Furthermore, we show that nonuniform sediment mixtures may result in a change in the direction of the hysteresis observed between sediment concentration and discharge (i.e., from a clockwise hysteresis to a counterclockwise hysteresis). We also demonstrate that the ratio between sediment distal supply and proximal sediment availability modulates the magnitude of the aggradation/degradation processes in the channel reach and thus the joint observations of sediment concentration and discharge.