Miracle-dz/UniFAR-FTUs huggingface dataset:
An Evolutionary Perspective on Single-Nucleotide Polymorphism Screening in Molecular Cancer Epidemiology

Given that there are millions of single-nucleotide polymorphisms (SNPs) in the entire human genome, a major difficulty faced by scientists in planning costly population-based genotyping is to choose target SNPs that are most likely to affect phenotypic functions and ultimately contribute to disease development. Although it is widely accepted that sequences with important functionality tend to be less variable across species because of selective pressure, to what extent evolutionary conservation is mirrored by epidemiological outcome has never been demonstrated. In this study, we surveyed odds ratios detected for 46 SNPs in 39 different cancer-related genes from 166 molecular epidemiological studies. The conservation levels of amino acid that these SNPs affected were calculated as a tolerance index by comparing sequences from different species. Our results provide evidence of a significant relationship between the detected odds ratios associated with cancer risk and the conservation levels of the SNP-affected amino acids (P = 0.002; R2 = 0.06). Tolerance indices were further calculated for 355 nonsynonymous SNPs identified in 90 human DNA repair genes, of which 103 caused amino acid changes in very conserved positions. Our findings support the concept that SNPs altering the conserved amino acids are more likely to be associated with cancer susceptibility. Using such a molecular evolutionary approach may hold great promise for prioritizing SNPs to be genotyped in future molecular epidemiological studies.
Taking the Next Step: Building an Arabidopsis Information Portal[OA]

The Arabidopsis Information Portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner.
Induction of Th17 cell differentiation by B-1 cells

B-1 cells constitute a unique B cell population with distinct ontogenic, phenotypic, and functional characteristics. Naïve, unmanipulated B-1 cells induce differentiation of CD4+ T cells to become pro-inflammatory Th17 cells whereas naïve B-2 cells do not. We examined the role of distinctly expressed surface membrane molecules in providing B-1 cells with Th17-differentiating function. Neither Mac-1, CD25, PD-L2 nor CD73 appeared to contribute to B-1 cell induction of Th17 differentiation. In contrast, we found that CD44 and CD86 are involved on the basis of studies with neutralizing antibodies and knock-out mice. Activation imparted to naïve B-2 cells the ability to induce Th17 differentiation and this was similarly partially interrupted by interfering with CD44 and CD86. Our findings suggest that CD44-OPN and B7 family members play important roles in the induction of Th17 cell differentiation by B cells.
The Diversity of Cassava Mosaic Begomoviruses in Africa

Cassava mosaic disease (CMD) is the most widespread and economically important disease of cassava (Manihot esculenta Crantz) in tropical Africa. A disease of cassava was first described in East Africa in the nineteenth century (Warburg, 1894) and cassava mosaic, as it came to be called, was subsequently reported as spreading throughout the cassava-growing areas of Central and West Africa (Calvert and Thresh, 2002). In more recent times, CMD has been reported as occurring at varying levels of incidence throughout the cassava belt of Africa and losses have been estimated at between 12% and 25% of total production (Thresh et al., 1997).
Association between Psoriasis and Chronic Obstructive Pulmonary Disease: A Systematic Review and Meta-analysis

Psoriasis is considered a systemic inflammatory disorder. Previous studies have reported conflicting positive or negative correlations between psoriasis and chronic obstructive pulmonary disease. We performed a meta-analysis to determine whether there is an associated risk between psoriasis and chronic obstructive pulmonary disease. We performed a complete 30-year literature search of MEDLINE, Embase, and Cochrane Central Register databases on this topic. Four observational studies with a total of 13,418 subjects were identified. The odds ratios of chronic obstructive pulmonary disease in subjects with psoriasis/mild-to-moderate psoriasis were analyzed using the random-effects model, while the odds ratios of chronic obstructive pulmonary disease in subjects with severe psoriasis and current smoking in subjects with psoriasis were analyzed using the fixed-effect model. We found that psoriasis patients were at a greater risk of developing chronic obstructive pulmonary disease than the general population (odds ratio, 1.90; 95% confidence interval, 1.36–2.65) and that the association between of psoriasis and with chronic obstructive pulmonary disease was stronger among patients with severe psoriasis (odds ratio, 2.15; 95% confidence interval, 1.26–3.67). Psoriasis patients should be advised to cease smoking to reduce their risk of COPD. Moreover, identification of this potential risk may enable earlier implementation of preventive measures for reduction comorbidity and mortality rates.
The Intention Interference Effect and Aging: Similar Magnitude of Effects for Young and Old Adults

SUMMARY In young adults, intentions have been shown to be more accessible (e.g. faster reaction times and higher accuracy) compared to other sorts of to-be-remembered information, a result termed an ‘intention superiority effect’ (Goschke & Kuhl, 1993). In the current study, we assessed whether older adults also demonstrate this superiority of intention-related material and we used a new interference paradigm to examine performance. On each trial, participants performed a Stroop-like colour-naming task on a short series of words, including words related to an intention that they encoded at the beginning of the trial. In Experiment 1, results revealed an ‘intention interference effect’ for both young and older adults in which performance was slower for words belonging to an intention that participants intended to carry out versus an intention that did not have to be executed. In Experiment 2, we tested the effect that completing an intention had on the representation of intentions. For both groups, completing an intention led to a decrease in interference in Stroop task performance. Copyright # 2005 John Wiley & Sons, Ltd.
Data mining based decomposition for assume-guarantee reasoning

Automated compositional reasoning using assume-guarantee rules plays a key role in large system verification. A vexing problem is to discover fine decomposition of system contributing to appropriate assumptions. We present an automatic decomposition approach in compositional reasoning verification. The method is based on data mining algorithms. An association rule algorithm is harnessed to discover the hidden rules among system variables. A hypergraph partitioning algorithm is proposed to incorporate these rules as weight constraints for system variable clustering. The experiments demonstrate that our strategy leads to order-of-magnitude speedup over previous.
Initial stage of isothermal decomposition of austenite to ferrite and graphite in spheroidal graphite cast iron

AbstractThe isothermal decomposition of austenite to ferrite and graphite in a spheroidal graphite cast iron was investigated by dilatometry, metallography, and image analysis. The results gave quantitative, although indirect, information on the kinetics of carbon transfer from austenite to graphite, as well as on the kinetics of the austenite to ferrite and graphite transformation. The relationship between the kinetics and the graphite nodule count was highlighted. The incubation period before ferrite growth was found to be associated with a global contraction of the material, in spite of the related increase in the graphite volume fraction. Calculations showed good agreement with experimental results, except for the rate of carbon transfer, which was found to be much slower experimentally than predicted by calculations based on the volume diffusion of carbon. Possible reasons for this discrepancy are discussed.
A Movement-Associated Fast Rolandic Rhythm

ABSTRACT: A stereotyped 32 Hz rolandic rhythm maximal over the mesial cortex and occurring only with voluntary movement is described in a patient with tonic postural seizures. This abnormal but nonictal rhythm, which is probably generated subcortically, is expressed synchronously at the level of the cortex and peripherally in the EMG.
SpiraList: a compact visualization technique for one-handed interaction with large lists on mobile devices

This paper presents SpiraList, a focus+context visualization technique for interacting with large lists on handheld devices. SpiraList has been specifically designed to fit the constraints of small tactile screens. It provides a global view of large lists by way of a compact layout based on a spiral representation. Its design also allows for direct interaction with fingers. The combination of this compact layout and one-handed interaction makes SpiraList particularly suitable for mobility.
Cell-Dependent Role for the Poliovirus 3′ Noncoding Region in Positive-Strand RNA Synthesis

ABSTRACT We previously reported the isolation of a mutant poliovirus lacking the entire genomic RNA 3′ noncoding region. Infection of HeLa cell monolayers with this deletion mutant revealed only a minor defect in the levels of viral RNA replication. To further analyze the consequences of the genomic 3′ noncoding region deletion, we examined viral RNA replication in a neuroblastoma cell line, SK-N-SH cells. The minor genomic RNA replication defect in HeLa cells was significantly exacerbated in the SK-N-SH cells, resulting in a decreased capacity for mutant virus growth. Analysis of the nature of the RNA replication deficiency revealed that deleting the poliovirus genomic 3′ noncoding region resulted in a positive-strand RNA synthesis defect. The RNA replication deficiency in SK-N-SH cells was not due to a major defect in viral translation or viral protein processing. Neurovirulence of the mutant virus was determined in a transgenic mouse line expressing the human poliovirus receptor. Greater than 1,000 times more mutant virus was required to paralyze 50% of inoculated mice, compared to that with wild-type virus. These data suggest that, together with a cellular factor(s) that is limiting in neuronal cells, the poliovirus 3′ noncoding region is involved in positive-strand synthesis during genome replication.
A preliminary study of factors influencing perception of articulatory rate in Parkinson disease.

This investigation was a preliminary study of factors influencing perception of articulatory rate in idiopathic Parkinson disease (PD). Nine men with mild to moderate idiopathic PD and 9 healthy men of a similar age read the Farm Passage at habitual, fast, and slow reading rates. Spontaneous speech samples also were obtained. Speech severity for participants with PD was mild to moderate; prominent perceptual characteristics further suggested hypokinetic dysarthria. Nine listeners estimated the articulatory rate of speech runs (i.e., stretch of speech bounded by pauses) extracted from the reading and spontaneous speech samples. Regression analysis was used to explore the relationship between articulatory rate (i.e., syllables produced per second excluding pauses) and perceptual impressions of articulatory rate as well as the relationship between fundamental frequency (F0) range and perceptual estimates of articulatory rate. Regression functions predicting perceptual estimates of articulatory rate from F0 range were not significant for either speaker group. The regression analyses relating articulatory rate and perceptual estimates of articulatory rate, however, revealed a significant, positive relationship between the two measures for both speaker groups. There also was a nonsignificant trend for perception of articulatory rate to grow more rapidly for Parkinsonian speech samples. Although the current findings should be interpreted with caution until they have been validated by additional studies using much larger speaker populations and more extensive speech samples, the results hint at the possibility that perceptual impressions of articulatory rate in PD may overestimate the actual, physical rate. The results also highlight the importance of speech-language pathologists complimenting perceptual judgements of articulatory rate with physical measures.
Regulatory T Cells in Arterivirus and Coronavirus Infections: Do They Protect Against Disease or Enhance it?

Regulatory T cells (Tregs) are a subset of T cells that are responsible for maintaining peripheral immune tolerance and homeostasis. The hallmark of Tregs is the expression of the forkhead box P3 (FoxP3) transcription factor. Natural regulatory T cells (nTregs) are a distinct population of T cells that express CD4 and FoxP3. nTregs develop in the thymus and function in maintaining peripheral immune tolerance. Other CD4+, CD4-CD8-, and CD8+CD28- T cells can be induced to acquire regulatory function by antigenic stimulation, depending on the cytokine milieu. Inducible (or adaptive) Tregs frequently express high levels of the interleukin 2 receptor (CD25). Atypical Tregs express FoxP3 and CD4 but have no surface expression of CD25. Type 1 regulatory T cells (Tr1 cells) produce IL-10, while T helper 3 cells (Th3) produce TGF-β. The function of inducible Tregs is presumably to maintain immune homeostasis, especially in the context of chronic inflammation or infection. Induction of Tregs in coronaviral infections protects against the more severe forms of the disease attributable to the host response. However, arteriviruses have exploited these T cell subsets as a means to dampen the immune response allowing for viral persistence. Treg induction or activation in the pathogenesis of disease has been described in both porcine reproductive and respiratory syndrome virus, lactate dehydrogenase elevating virus, and mouse hepatitis virus. This review discusses the development and biology of regulatory T cells in the context of arteriviral and coronaviral infection.
Papyrus reinforced poly(L-lactic acid) composite

Mechanical reinforcement of an all-sustainable composite, composed of papyrus stem-milled particles as reinforcement and poly-L-lactic acid (PLLA) resin as matrix, was investigated. The papyrus particles (average diameter of 70 μm) could be well dispersed in PLLA resin up to 50 wt% without any surface modification. Young's modulus of the composite was 4.2 GPa at 50 wt% of the papyrus content. This is a two-fold increment in modulus as compared to that of the PLLA matrix. The tensile strength of the composite was almost constant around 48 MPa irrespective of the papyrus content. Temperature dependence of the storage modulus demonstrated that the incorporation of papyrus restricts the large drop in the modulus above the glass transition of PLLA.
Porous Hydrogen-Bonded Organic Frameworks

Ordered porous solid-state architectures constructed via non-covalent supramolecular self-assembly have attracted increasing interest due to their unique advantages and potential applications. Porous metal-coordination organic frameworks (MOFs) are generated by the assembly of metal coordination centers and organic linkers. Compared to MOFs, porous hydrogen-bonded organic frameworks (HOFs) are readily purified and recovered via simple recrystallization. However, due to lacking of sufficiently ability to orientate self-aggregation of building motifs in predictable manners, rational design and preparation of porous HOFs are still challenging. Herein, we summarize recent developments about porous HOFs and attempt to gain deeper insights into the design strategies of basic building motifs.
Intercellular Spreading of Porphyromonas gingivalis Infection in Primary Gingival Epithelial Cells

ABSTRACT Porphyromonas gingivalis, an important periodontal pathogen, is an effective colonizer of oral tissues. The organism successfully invades, multiplies in, and survives for extended periods in primary gingival epithelial cells (GECs). It is unknown whether P. gingivalis resides in the cytoplasm of infected cells throughout the infection or can spread to adjacent cells over time. We developed a technique based on flow cytofluorometry and fluorescence microscopy to study propagation of the organism at different stages of infection of GECs. Results showed that P. gingivalis spreads cell to cell and that the amount of spreading increases gradually over time. There was a very low level of propagation of bacteria to uninfected cells early in the infection (3 h postinfection), but there were 20-fold and 45-fold increases in the propagation rate after 24 h and 48 h, respectively, of infection. Immunofluorescence microscopy of infected cells suggested that intercellular translocation of P. gingivalis may be mediated through actin-based membrane protrusions, bypassing the need for release of bacteria into extracellular medium. Consistent with these observations, cytochalasin D treatment of infected cells resulted in significant inhibition of bacterial spreading. This study shows for the first time that P. gingivalis disseminates from cell to cell without passing through the extracellular space. This mechanism of spreading may allow P. gingivalis to colonize oral tissues without exposure to the humoral immune response.
Variation in Lunar Neutron Dose Estimates

The radiation environment on the Moon includes albedo neutrons produced by primary particles interacting with the lunar surface. In this work, HZETRN2010 is used to calculate the albedo neutron contribution to effective dose as a function of shielding thickness for four different space radiation environments and to determine to what extent various factors affect such estimates. First, albedo neutron spectra computed with HZETRN2010 are compared to Monte Carlo results in various radiation environments. Next, the impact of lunar regolith composition on the albedo neutron spectrum is examined, and the variation on effective dose caused by neutron fluence-to-effective dose conversion coefficients is studied. A methodology for computing effective dose in detailed human phantoms using HZETRN2010 is also discussed and compared. Finally, the combined variation caused by environmental models, shielding materials, shielding thickness, regolith composition and conversion coefficients on the albedo neutron contribution to effective dose is determined. It is shown that a single percentage number for characterizing the albedo neutron contribution to effective dose can be misleading. In general, the albedo neutron contribution to effective dose is found to vary between 1–32%, with the environmental model, shielding material and shielding thickness being the driving factors that determine the exact contribution. It is also shown that polyethylene or other hydrogen-rich materials may be used to mitigate the albedo neutron exposure.
Selectively Convertible Authenticated Encryption in the Random Oracle Model

Conventionally, a verified digital signature releases information about both the signing event and the signed content simultaneously, where the signing event proves the truth that someone actually signed something. However, in many cases, the information of the signing event and the signed content have different uses and distinct degrees of importance on various occasions. In such cases, the conventional digital signature, the current authenticated encryption schemes and the current signcryption schemes cannot satisfy the needs of selectively releasing either the information about the signing event or that about the signed content or both depending on the situation. In this paper, we shall propose a selectively convertible authenticated encryption scheme where either the sender or the designated receiver can selectively convert the encryption such that the signing event and that of the signed content can be released adaptively. The security of the scheme is proved in the random oracle model. Applications based on the proposed scheme are also introduced.
Olfactory ensheathing cell transplantation improves sympathetic skin responses in chronic spinal cord injury

Forty-three patients with chronic spinal cord injury for over 6 months were transplanted with bryonic olfactory ensheathing cells, 2–4 × 106, into multiple sites in the injured area under the surgical microscope. The sympathetic skin response in patients was measured with an electromyography/evoked potential instrument 1 day before transplantation and 3–8 weeks after transtion. Spinal nerve function of patients was assessed using the American Spinal Injury Association impairment scale. The sympathetic skin response was elicited in 32 cases before olfactory ensheathing cell transplantation, while it was observed in 34 cases after transplantation. tantly, sympathetic skin response latency decreased significantly and amplitude increased cantly after transplantation. Transplantation of olfactory ensheathing cells also improved American Spinal Injury Association scores for movement, pain and light touch. Our findings indicate that factory ensheathing cell transplantation improves motor, sensory and autonomic nerve functions in patients with chronic spinal cord injury.
RanBP3 enhances nuclear export of active β-catenin independently of CRM1

β-Catenin is the nuclear effector of the Wnt signaling cascade. The mechanism by which nuclear activity of β-catenin is regulated is not well defined. Therefore, we used the nuclear marker RanGTP to screen for novel nuclear β-catenin binding proteins. We identified a cofactor of chromosome region maintenance 1 (CRM1)–mediated nuclear export, Ran binding protein 3 (RanBP3), as a novel β-catenin–interacting protein that binds directly to β-catenin in a RanGTP-stimulated manner. RanBP3 inhibits β-catenin–mediated transcriptional activation in both Wnt1- and β-catenin–stimulated human cells. In Xenopus laevis embryos, RanBP3 interferes with β-catenin–induced dorsoventral axis formation. Furthermore, RanBP3 depletion stimulates the Wnt pathway in both human cells and Drosophila melanogaster embryos. In human cells, this is accompanied by an increase of dephosphorylated β-catenin in the nucleus. Conversely, overexpression of RanBP3 leads to a shift of active β-catenin toward the cytoplasm. Modulation of β-catenin activity and localization by RanBP3 is independent of adenomatous polyposis coli protein and CRM1. We conclude that RanBP3 is a direct export enhancer for β-catenin, independent of its role as a CRM1-associated nuclear export cofactor.