Miracle-dz/UniFAR-FTUs huggingface dataset:
Transitioning Out of the Coronavirus Lockdown: A Framework for Evaluating Zone-Based Social Distancing

In the face of elevated pandemic risk, canonical epidemiological models imply the need for extreme social distancing over a prolonged period. Alternatively, people could be organized into zones, with more interactions inside their zone than across zones. Zones can deliver significantly lower infection rates, with less social distancing, particularly if combined with simple quarantine rules and contact tracing. This paper provides a framework for understanding and evaluating the implications of zones, quarantines, and other complementary policies.
Bioinformatics Analysis of Prognostic miRNA Signature and Potential Critical Genes in Colon Cancer

This study aims to lay a foundation for studying the regulation of microRNAs (miRNAs) in colon cancer by applying bioinformatics methods to identify miRNAs and their potential critical target genes associated with colon cancer and prognosis. Data of differentially expressed miRNAs (DEMs) and genes (DEGs) downloaded from two independent databases (TCGA and GEO) and analyzed by R software resulted in 472 DEMs and 565 DEGs in colon cancers, respectively. Next, we developed an 8-miRNA (hsa-mir-6854, hsa-mir-4437, hsa-mir-216a, hsa-mir-3677, hsa-mir-887, hsa-mir-4999, hsa-mir-34b, and hsa-mir-3189) prognostic signature for patients with colon cancer by Cox proportional hazards regression analysis. To predict the target genes of these miRNAs, we used TargetScan and miRDB. The intersection of DEGs with the target genes predicted for these eight miRNAs retrieved 112 consensus genes. GO and KEGG pathway enrichment analyses showed these 112 genes were mainly involved in protein binding, one-carbon metabolic process, nitrogen metabolism, proteoglycans in cancer, and chemokine signaling pathways. The protein–protein interaction network of the consensus genes, constructed using the STRING database and imported into Cytoscape, identified 14 critical genes in the pathogenesis of colon cancer (CEP55, DTL, FANCI, HMMR, KIF15, MCM6, MKI67, NCAPG2, NEK2, RACGAP1, RRM2, TOP2A, UBE2C, and ZWILCH). Finally, we verified the critical genes by weighted gene co-expression network analysis (WGCNA) of the GEO data, and further mined the core genes involved in colon cancer. In summary, this study identified an 8-miRNA model that can effectively predict the prognosis of colon cancer patients and 14 critical genes with vital roles in colon cancer carcinogenesis. Our findings contribute new ideas for elucidating the molecular mechanisms of colon cancer carcinogenesis and provide new therapeutic targets and biomarkers for future treatment and prognosis.
Biogenesis of type I cytopathic vacuoles in Semliki Forest virus-infected BHK cells

We investigated the biogenesis of type I cytopathic vacuoles (CPVIs) in Semliki Forest virus (SFV)-infected cells by immunofluorescence and electron microscopy. By using the ts1 mutant of SFV at the restrictive temperature to avoid superinfection, we showed that the multiplicity of infection affects the time of appearance but not the number of CPVIs in a cell. Formation of CPVIs did not require incoming virus particles, because they were found in BHK cells transfected with infectious RNA from the SFV prototype strain or ts1 mutant. When the SFV gene for nsP3 was expressed alone in BHK cells, the nsP3 protein was localized to numerous vesiclelike structures and large vacuoles. The nsP3 protein may function as an anchoring protein for the RNA replication complex of SFV.
Indentation-Induced Structural Changes in Vitreous Silica Probed by in-situ Small-Angle X-Ray Scattering

The transient (or permanent) structural modifications which occur during local deformation of oxide glasses are typically studied on the basis of short-range data, for example, obtained through vibrational spectroscopy. This is in contrast to macroscopic observations, where variations in material density can usually not be explained using next-neighbor correlations alone. Recent experiments employing low-frequency Raman spectroscopy have pointed-out this issue, emphasizing that the deformation behavior of glasses is mediated through structural heterogeneity and drawing an analogy to granular media. Here, we provide additional support to this understanding, using an alternative experimental method. Structural modification of vitreous silica in the stress field of a sharp diamond indenter tip was monitored by in-situ small-angle X-ray scattering. The influenced zone during loading and after unloading was compared, demonstrating that changes in the position of the first sharp diffraction peak (FSDP) directly in the center of the indent are of permanent character. On the other hand, variations in the amplitude of electron density fluctuations (AEDF) appear to fully recover after load release. The lateral extent of the modifications and their relaxation are related to the short- to intermediate-range structure and elastic heterogeneity pertinent to the glass network. With support from Finite Element Analysis, we suggest that different structural length scales govern shear deformation and isotropic compaction in vitreous silica.
EFFECTIVE COHERENCE LENGTH ESTIMATION OF OPTICAL WAVEFRONTS

In adaptive optics, the measurement of spatial coherence length helps in deciding the optimum design parameters of a Shack Hartmann Sensor (SHS). Two methods of estimating the spatial coherence length of optical wavefronts are presented. The first method is based on counting the number of Hough peaks in the wavefront. The second method is based on a simple data mining technique applied on the wavefronts. Optical wavefronts with different properties are simulated and used for statistical analysis. A comparison of the performance of the two methods is presented using Monte Carlo simulations. It is shown that both these methods can become efficient tools in estimating the effective coherence length of optical wavefronts.
Angiokeratoma Circumscriptum Naeviforme: Successful Treatment with Carbon‐Dioxide Laser Vaporization

BACKGROUND Angiokeratoma circumscriptum naeviforme (ACN) is an unusual type of localized angiokeratoma that occurs more frequently in females and is usually located on the buttocks or thighs, showing a unilateral distribution. ACN usually causes large lesions, which may require laser ablation because they often are too extensive to perform surgical excision. Carbon-dioxide laser is a known alternative for treating angiokeratomas. OBJECTIVE Report of two cases of ACN treated with carbon-dioxide laser vaporization. PATIENTS AND METHODS A 28-year-old woman with a hyperkeratotic, violaceus plaque on her left buttock and a 24-year-old woman with a similar lesion on her right buttock were treated with a carbon-dioxide laser. Two laser passes were performed on each lesion within a single session. RESULTS A successful cosmetic aspect of treated areas was obtained, with minimal pigmentary or textural changes. After a 2-year follow-up in the first patient and a 6-month follow-up in the second patient, no recurrence of the lesions was observed. CONCLUSIONS Our results, obtaining relevant cosmetic improvement after a few sessions of treatment, with low morbidity and minimal secondary effects, suggest that continuous-wave carbon-dioxide laser vaporization is a safe and effective treatment for ACN.
The DNA-dependent ATPase Activity of Yeast Nucleotide Excision Repair Factor 4 and Its Role in DNA Damage Recognition*

Saccharomyces cerevisiae RAD7 andRAD16 genes function together in the nucleotide excision repair of transcriptionally inactive DNA. The RAD7- andRAD16-encoded proteins exist as a tight complex named nucleotide excision repair factor 4 or NEF4. Previously, we showed that NEF4 binds UV-damaged DNA with high specificity and with a dependence upon ATP and that inclusion of NEF4 to the reconstituted nucleotide excision repair system consisting of purified NEF1, NEF2, NEF3, and replication protein A results in marked stimulation of damage-specific DNA incision. Here we show that NEF4 possesses an ATPase activity that is entirely dependent on a DNA cofactor and that double-stranded DNA is twice as effective as single-stranded DNA in activating ATP hydrolysis. Even though DNA binding is promoted by the nonhydrolyzable ATP analogue adenosine 5′-O-(thiotriphosphate) (ATPγS), damage binding is more proficient with ATP than with ATPγS. Interestingly, UV irradiation of double-stranded DNA results in a pronounced attenuation of the ATPase activity. Taken together, our results suggest a model in which ATP hydrolysis by NEF4 fuels the translocation of NEF4 on DNA in search of UV lesions and damage binding by NEF4 leads to a down-regulation of the ATPase activity. Damage-bound NEF4 could then serve as a nucleation point for the assembly of other repair components.
Multifaceted interaction between the androgen and Wnt signaling pathways and the implication for prostate cancer

Androgen action in prostate and prostate cancer cells is dependent upon the androgen receptor (AR) protein that transcriptionally regulates the expression of androgen‐dependent genes in the presence of a steroid ligand. Whereas the overall schema of androgen action mediated by this receptor protein appears to be relatively simple, androgen signaling is now known to be influenced by several other cell signal transduction pathways and here we review the evidence that the canonical Wnt signaling pathway also modulates androgen signaling at multiple levels. Wnt is a complex signaling pathway whose endpoint involves activation of transcription from LEF‐1/TCF transcription factors and it is known to be involved in the development and progression of numerous human epithelial tumors including prostate cancer. β‐catenin protein, a particularly critical molecular component of canonical Wnt signaling is now known to promote androgen signaling through its ability to bind to the AR protein in a ligand‐dependent fashion and to enhance the ability of liganded AR to activate transcription of androgen‐regulated genes. Under certain conditions, glycogen synthase kinase‐3β (GSK‐3β), a protein serine/threonine kinase that regulates β‐catenin degradation within the Wnt signaling pathway, can also phosphorylate AR and suppress its ability to activate transcription. Finally, it was recently found that the human AR gene itself is a target of LEF‐1/TCF‐mediated transcription and that AR mRNA is highly upregulated by activation of Wnt signaling in prostate cancer cells. Paradoxically, Wnt activation also appears to stimulate Akt activity promoting an MDM‐2‐mediated degradation process that reduces AR protein levels in Wnt‐stimulated prostate cancer cells. Collectively, this information indicates that the multifaceted nature of the interaction between the Wnt and the androgen signaling pathways likely has numerous consequences for the development, growth, and progression of prostate cancer. J. Cell. Biochem. 99: 402–410, 2006. © 2006 Wiley‐Liss, Inc.
Hopfield net generation, encoding and classification of temporal trajectories

Hopfield network transient dynamics have been exploited for resolving both path planning and temporal pattern classification. For these problems Lagrangian techniques and two well-known learning algorithms for recurrent networks have been used. For path planning, the Williams and Zisper's learning algorithm has been implemented and a set of temporal trajectories which join two points, pass through others, avoid obstacles and jointly form the shortest path possible are discovered and encoded in the weights of the net. The temporal pattern classification is based on an extension of the Pearlmutter's algorithm for the generation of temporal patterns which is obtained by means of variational methods. The algorithm is applied to a simple problem of recognizing five temporal trajectories with satisfactory robustness to distortions.
Phosphatidylinositol-specific phospholipase C, a possible virulence factor of Staphylococcus aureus

Phosphatidylinositol-specific phospholipase C (PIPLC), an enzyme that can specifically release phosphatidylinositol-linked proteins from host cells, is one of the extracellular enzymes produced by Staphylococcus aureus. To investigate whether PIPLC might be a virulence factor, we assessed PIPLC production by S. aureus strains that had been isolated from healthy carriers and from infected patients with or without toxic shock syndrome. Although none of five vaginal isolates from healthy women was a PIPLC producer, only 10 of 32 selected pathogenic strains that caused significant infections or toxic shock syndrome elaborated PIPLC enzyme activity. Seven of 24 toxic-shock-associated strains, compared with 3 of 8 non-toxic-shock-associated strains, were positive for PIPLC. The majority of strains that produced PIPLC were negative for toxic shock syndrome toxin 1 (P less than 0.05); this association between PIPLC production and strains negative for toxic shock syndrome toxin 1 was even stronger among strains isolated only from patients with toxic shock syndrome (P less than 0.01). Among all 32 pathogenic isolates, PIPLC-producing S. aureus strains were isolated from four of four patients developing adult respiratory distress syndrome and four of five patients with disseminated intravascular coagulation, suggesting a significant association between PIPLC production and adult respiratory distress syndrome and/or disseminated intravascular coagulation (P less than 0.002). On the basis of these results, we propose that PIPLC is a virulence factor of S. aureus and is implicated in the development of adult respiratory distress syndrome and disseminated intravascular coagulation.
The long-lasting effect caused by direct current for somatosensory evoked potentials and high frequency oscillations

The long-term effects for the neural activities on somatosensory area caused by transcranial direct current stimulation (tDCS) have been showed with somatosensory evoked potentials (SEPs) and high frequency oscillations (HFOs) in animals and humans. This study investigates the relationship of SEPs with HFOs before and after applying cathodal tDCS (0, 15, 30, 45, 60 min) to human left somatosensory cortex for 15 min at 2 mA. The amplitudes of N20 and P30 evoked by right median nerve stimulation were slightly decreased after cathodal tDCS. Likewise, HFOs were affected by cathodal tDCS but there weren't steadily decrement during the entire HFO, the effects were oscillating depending on the peak of HFOs or the elapse time after tDCS. tDCS may leave the different influences between time- and location-dependent somatosensory processing.
A variation in the organization of abductor pollicis longus

The abductor pollicis longus (APL) muscle has been studied bilaterally in 50 cadavers. A variation in the organization of the muscle was found bilaterally in 15 of the 50 specimens. The novel muscular arrangement gives the appearance of being an additional muscle belly arising from the lateral aspect of the distal portion of the typical abductor pollicis longus muscle belly. This variation in the arrangement also creates a retinacular‐like tunnel which encases the tendons of the extensor carpi radialis longus and the extensor carpi radialis brevis muscles. To the authors' knowledge, this arrangement has not been cited in the recent medical literature. An understanding of this unusual finding may be clinically relevant in describing the dorso‐lateral compartment of the distal forearm. © 1996 Wiley‐Liss, Inc.
DeepCrop : Directed Object Segmentation with Deep Learning

When editing a photo, the ability to click on an object and crop it from the rest of the photo ’directed object segmentation’ would be useful. A lot of progress has recently been made on the related task of un-directed object segmentation (producing outlines for all objects within an image), and in particular Pinheiro et al. ”DeepMask” recently achieved state of art results for this problem with a deep learning model[7]. A similar model to DeepMask, with the addition of a pixel coordinate input that is within the bounds of the object to segment from the rest of the image, can be trained for directed object segmentation. I implemented and evaluated two variations of this model, referred to as ’DeepCrop’. The second version of DeepCrop was shown to train faster and perform slightly better on images that are cropped as in during training, and a demo was developed for a qualitative evaluation of segmentation within an entire image.
Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients

The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We propose that natural selection has favored a “Don’t burn down the house” strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.
Inhibitory effect of cranberry extract on periodontopathogenic biofilm: An integrative review

Background: Combating biofilm-dependent oral infections involves the use of synthetic antibiotics, which are often associated with bacterial resistance and adverse effects. As a result, herbs such as cranberry have emerged as an alternative treatment. The aim of this study was to evaluate, through an integrative literature review, the effectiveness of cranberry extract on cultures and biofilms of periodontopathogenic bacteria. Materials and Methods: In vitro and in vivo studies evaluating the action of cranberry extract on the growth, coaggregation and formation of periodontopathogenic bacteria and periodontal biofilm were identified. Searches were carried out in the “Cochrane Library,” “MEDLINE,” “Web of Science,” “Scopus,” “LILACS,” “Scielo,” and “Google Scholar” databases, using the terms: “vaccinium macrocarpon;” “cranberries;” “cranberry;” “biofilms;” “periodontitis;” “chronic periodontitis;” “aggressive periodontitis;” “periodontal diseases;” and “periodont*. ” Results: a low number of studies evaluating the effectiveness of cranberry extract on periodontal disease were found, and no human studies were identified. In general, the eight studies included in the revision found that the compounds effectively inhibited the formation of a biofilm of Porphyromonas gingivalis and Fusobacterium nucleatum at concentrations equal or superior to 62.5 μg/ml, but did not significantly inhibit bacterial growth or promote the breakdown of preformed biofilm. Conclusions: while most of the studies presented certain methodological limitations, they did identify an inhibiting effect of cranberry on periodontal bacteria. These results serve as support for the development of further studies evaluating the most effective vehicle and ideal concentration that can be used without causing adverse effects on oral tissues.
Chronic ulcers of the leg of venous origin.

I is estimated that 600,000 ulcers of the leg are treated annually in the United States —an estimate that is extrapolated from a reported incidence of 15,000 ulcers of the leg treated annually in Denmark. These vast numbers argue a problem, the magnitude of which never has been evaluated in terms of physical disability and economic loss both to the individual and to the community. This study will present the current beliefs and practices in regard to the origin and treatment of the disease.
Restriction Fragment Length Polymorphisms in the Mushrooms Agaricus brunnescens and Agaricus bitorquis

Two Agaricus species, A. brunnescens (a commercial mushroom) and A. bitorquis (a wild, edible species), were examined for restriction fragment length polymorphisms. EcoRI-digested nuclear DNA from isolates of both species were cloned in plasmid vector pUC18. Ten random recombinant clones were used in Southern DNA-DNA hybridizations to probe EcoRI-digested DNA from 11 A. brunnescens isolates (7 commercial, 2 wild type, and 2 homokaryotic) and 7 A. bitorquis isolates. Most cloned fragments were polymorphic in both species. There were fewer different genotypes than expected, however, in the sample of commercial A. brunnescens strains. DNA from homokaryotic strains showed fewer bands in most hybridizations than DNA from heterokaryotic strains. All A. bitorquis isolates could be distinguished from each other as well as from every A. brunnescens strain. Putative homokaryons were detected by the loss of polymorphic bands among protoplast regenerates from one commercial strain and two strains collected in the wild.
Is the Performance of Acceleromyography Improved with Preload and Normalization?: A Comparison with Mechanomyography

Background:Many studies have indicated that acceleromyography and mechanomyography cannot be used interchangeably. To improve the agreement between the two methods, it has been suggested to use a preload and to refer all train-of-four (TOF) ratios to the control TOF (normalization) when using acceleromyography. The first purpose of this study was to test whether a preload applied to acceleromyography would increase the precision and the agreement with mechanomyography. The second purpose was to evaluate whether normalization would improve the agreement with mechanomyography. Methods:Sixty patients were randomized to acceleromyography with or without a preload (Hand Adapter; Organon, Oss, the Netherlands). On the contralateral arm, mechanomyography was used. Anesthesia was induced with propofol and an opioid, and neuromuscular block with 0.6 mg/kg rocuronium. The precision and the bias and limits of agreement (with or without normalization) between the methods were evaluated using TOF stimulation. Results:Preload improved the precision of acceleromyography by 21%, but it also increased the mean control TOF ratio from 1.07 to 1.13. Normalization of the acceleromyographic TOF ratios diminished the bias to mechanomyography during recovery (e.g., from 0.15 to 0.05 at TOF 0.90); when the mechanomyographic TOF values were normalized as well, the bias was eliminated. However, normalization did not exclude wide individual differences between acceleromyography and mechanomyography (± 0.10–0.20 at TOF 0.90). Conclusion:Preload increases the precision of acceleromyography, and normalization of the TOF ratios decreases bias in relation to mechanomyography. When both acceleromyography and mechanomyography are normalized, there is no significant bias between the two methods.