Miracle-dz/UniFAR-FTUs huggingface dataset:
Atmospheric Chemistry and Physics Discussions Interactive comment on “ Investigation of molar volume and surfactant characteristics of water-soluble organic compounds in biomass burning aerosol ”

This manuscript applies the newly developed Kohler Theory Analysis (KTA) method to estimate the average thermodynamic properties (i.e., molar volume, molecular weight) for organic species obtained from collected aerosol particles. The analysis relies on CCN activity and surface tension measurements which help eventually to estimate the average molecular weight of these organics. It is shown that the more hydrophobic fractions of these organics are more surface-active then the low molecular weight hydrophilic part, and may represent humic like species (HULIS). The manuscript also makes a nice use of the salting out effect in order to probe the effect of surface tension on activation. In addition, the authors provide an estimate of the molecular weight of the organic species, which suggests evidence for atmospheric processing. The paper
The Origin of the RB1 Imprint

The human RB1 gene is imprinted due to a differentially methylated CpG island in intron 2. This CpG island is part of PPP1R26P1, a truncated retrocopy of PPP1R26, and serves as a promoter for an alternative RB1 transcript. We show here by in silico analyses that the parental PPP1R26 gene is present in the analysed members of Haplorrhini, which comprise Catarrhini (Old World Monkeys, Small apes, Great Apes and Human), Platyrrhini (New World Monkeys) and tarsier, and Strepsirrhini (galago). Interestingly, we detected the retrocopy, PPP1R26P1, in all Anthropoidea (Catarrhini and Platyrrhini) that we studied but not in tarsier or galago. Additional retrocopies are present in human and chimpanzee on chromosome 22, but their distinct composition indicates that they are the result of independent retrotransposition events. Chimpanzee and marmoset have further retrocopies on chromosome 8 and chromosome 4, respectively. To examine the origin of the RB1 imprint, we compared the methylation patterns of the parental PPP1R26 gene and its retrocopies in different primates (human, chimpanzee, orangutan, rhesus macaque, marmoset and galago). Methylation analysis by deep bisulfite sequencing showed that PPP1R26 is methylated whereas the retrocopy in RB1 intron 2 is differentially methylated in all primates studied. All other retrocopies are fully methylated, except for the additional retrocopy on marmoset chromosome 4, which is also differentially methylated. Using an informative SNP for the methylation analysis in marmoset, we could show that the differential methylation pattern of the retrocopy on chromosome 4 is allele-specific. We conclude that the epigenetic fate of a PPP1R26 retrocopy after integration depends on the DNA sequence and selective forces at the integration site.
Histological response to cylinders of a low modulus titanium alloy (Ti‐13Nb‐13Zr) and a wear resistant zirconium alloy (Zr‐2.5Nb) implanted in the rabbit tibia

To assess new and existing materials for total joint arthroplasty, the authors performed a comprehensive histomorphologic and morphometric analysis of bone to cylinders implanted transversely in the proximal tibia of mature New Zealand white rabbits. Four sterile, cylindrical implants measuring 6.1 × 3.8mm were manually inserted through drill holes in both tibiae with a „line-to-line fit. ” The materials tested included: ASTM F-75 cast cobalt-chrome-molybdenum alloy, commercially pure titanium wrought zirconium-2.5 niobium alloy, zirconium oxide coated zirconium-2.5 niobium alloy, wrought titanium-13 niobium-13 zirconium alloy, and nitrogen diffusion hardened titanium-6 aluminum-4 vanadium alloy. Control animals with or without drill holes were included. The animals were killed by barbiturate overdose 6 months postoperatively. The upper tibiae were harvested and processed for undecalcified histologic sections that were stained with toluidine blue. The sections were examined by an investigator blind to the identity of the implanted materials. A full necropsy was also performed. A collar of lamellar bone, of variable length and thickness, continuous with the original cortex formed a buttress around the implants. There was no evidence of foreign body or inflammatory reaction. The marrow was slightly fatty, but cells of allthree hematopoietic lines were identifiable. The materials investigated had the following ranking in decreasing order of bone contact: Ti-13Nb-13Zr > nitrogen hardened Ti-6Al-4V > C.P. titanium > Zr 2.5Nb >ZrO2 coated Zr-2.5Nb > cast CoCr alloy. The difference between the groups was statistically significant (p = 0.05). For the variable „average bone layer thickness” the ranking in decreasing order was: nitrogen hardened Ti-6Al-4V alloy = C.P. titanium > Ti-13Nb-13Zr > ZrO2/Zr-2.5Nb > Zr-2.5Nb > cast CoCr alloy (p = 0.19). For the variable „average bone layer thickness in bone contact regions,” the ranking of the values, in decreasing order were: nitrogen hardened Ti-6Al-4V > C.P. titanium > ZrO2 coated Zr-2.5Nb > Ti-13Nb-13Zr >Zr-2.5 Nb > cast CoCr alloy (p = 0.02). The final necropsy reports of the animals identified no adverse findings that were concentrated to any particular implant group. The new, lower modulus materials Ti-13Nb-13Zr and Zr-2.5 Nb, and nitrogen hardened Ti-6Al-4V appear to have a similar or superior bone response to CoCr alloy when implanted in the rabbit tibia model. © 1993 John Wiley & Sons, Inc.
A structural perspective on the interactions of TRAF6 and Basigin during the onset of melanoma: A molecular dynamics simulation study

Metastatic melanoma is the most fatal type of skin cancer. The roles of matrix metalloproteinases (MMPs) have well been established in the onset of melanoma. Basigin (BSG) belongs to the immunoglobulin superfamily and is critical for induction of extracellular MMPs during the onset of various cancers including melanoma. Tumor necrosis factor receptor‐associated factor 6 (TRAF6) is an E3‐ligase that interacts with BSG and mediates its membrane localization, which leads to MMP expression in melanoma cells. This makes TRAF6 a potential therapeutic target in melanoma. We here conducted protein‐protein interaction studies on TRAF6 and BSG to get molecular level insights of the reactions. The structure of human BSG was constructed by protein threading. Molecular‐docking method was applied to develop the TRAF6‐BSG complex. The refined docked complex was further optimized by molecular dynamics simulations. Results from binding free energy, surface properties, and electrostatic interaction analysis indicate that Lys340 and Glu417 of TRAF6 play as the anchor residues in the protein interaction interface. The current study will be helpful in designing specific modulators of TRAF6 to control melanoma metastasis.
Modular Curvature for Noncommutative Two-Tori

In this paper we investigate the curvature of conformal deformations by noncommutative Weyl factors of a flat metric on a noncommutative 2-torus, by analyzing in the framework of spectral triples functionals associated to perturbed Dolbeault operators. The analogue of Gaussian curvature turns out to be a sum of two functions in the modular operator corresponding to the non-tracial weight defined by the conformal factor, applied to expressions involving derivatives of the same factor. The first is a generating function for the Bernoulli numbers and is applied to the noncommutative Laplacian of the conformal factor, while the second is a two-variable function and is applied to a quadratic form in the first derivatives of the factor. Further outcomes of the paper include a variational proof of the Gauss-Bonnet theorem for noncommutative 2-tori, the modular analogue of Polyakov's conformal anomaly formula for regularized determinants of Laplacians, a conceptual understanding of the modular curvature as gradient of the Ray-Singer analytic torsion, and the proof using operator positivity that the scale invariant version of the latter assumes its extreme value only at the flat metric.
Cation-Induced Transcriptional Regulation of the dlt Operon of Staphylococcus aureus

ABSTRACT Lipoteichoic and wall teichoic acids (TA) are highly anionic cell envelope-associated polymers containing repeating polyglycerol/ribitol phosphate moieties. Substitution of TA with d-alanine is important for modulation of many cell envelope-dependent processes, such as activity of autolytic enzymes, binding of divalent cations, and susceptibility to innate host defenses. d-Alanylation of TA is diminished when bacteria are grown in medium containing increased NaCl concentrations, but the effects of increased salt concentration on expression of the dlt operon encoding proteins mediating d-alanylation of TA are unknown. We demonstrate that Staphylococcus aureus transcriptionally represses dlt expression in response to high concentrations of Na+ and moderate concentrations of Mg2+ and Ca2+ but not sucrose. Changes in dlt mRNA are induced within 15 min and sustained for several generations of growth. Mg2+-induced dlt repression depends on the ArlSR two-component system. Northern blotting, reverse transcription-PCR, and SMART-RACE analyses suggest that the dlt transcript begins 250 bp upstream of the dltA start codon and includes an open reading frame immediately upstream of dltA. Chloramphenicol transacetylase transcriptional fusions indicate that a region encompassing the 171 to 325 bp upstream of dltA is required for expression and Mg2+-induced repression of the dlt operon in S. aureus.
Sessionlock: securing web sessions against eavesdropping

Typical web sessions can be hijacked easily by a network eavesdropper in attacks that have come to be designated "sidejacking. " The rise of ubiquitous wireless networks, often unprotected at the transport layer, has significantly aggravated this problem. While SSL can protect against eavesdropping, its usability disadvantages often make it unsuitable when the data is not considered highly confidential. Most web-based email services, for example, use SSL only on their login page and are thus vulnerable to sidejacking. We propose SessionLock, a simple approach to securing web sessions against eavesdropping without extending the use of SSL. SessionLock is easily implemented by web developers using only JavaScript and simple server-side logic. Its performance impact is negligible, and all major web browsers are supported. Interestingly, it is particularly easy to implement on single-page AJAX web applications, e.g. Gmail or Yahoo mail, with approximately 200 lines of JavaScript and 60 lines of server-side verification code.
Regulation of gene expression by glucose

Purpose of the reviewIn addition to its metabolic function, glucose modulates gene expression which is crucial in adapting cells to variations in glycaemia. We summarize recent advances in our understanding of regulation of gene expression by glucose. Recent findingsIn-vivo and in-vitro experiments demonstrated that glucose regulates the transcription of genes encoding not only lipogenic and glycolytic enzymes but also proteins involved in global cell functions. The molecular mechanisms have begun to be elucidated, and the transcription factor carbohydrate responsive element-binding protein has emerged as a key actor, at least in liver. More recently, other candidates have been proposed, such as liver X receptors. In pathological situations, altered glycaemic control, as observed in diabetes mellitus, is associated with increased risk for microvascular and macrovascular complications. Recent findings suggest that changes in gene expression occurring in response to hyperglycaemia represent a novel component of glucotoxicity. SummaryUntil recently, the direct transcriptional effects of glucose were underestimated, and insulin was considered to be the major regulator of gene expression in response to glycaemic variation. The recent discovery and characterization of transcription factors mediating the glucose response demonstrate that glucose, like fatty acids and other key nutrients, can directly control gene expression.
Functional Evidence for a Cerebellar Node of the Dorsal Attention Network

The “dorsal attention network” or “frontoparietal network” refers to a network of cortical regions that support sustained attention and working memory. Recent work has demonstrated that cortical nodes of the dorsal attention network possess intrinsic functional connections with a region in ventral cerebellum, in the vicinity of lobules VII/VIII. Here, we performed a series of task-based and resting-state fMRI experiments to investigate cerebellar participation in the dorsal attention network in humans. We observed that visual working memory and visual attention tasks robustly recruit cerebellar lobules VIIb and VIIIa, in addition to canonical cortical dorsal attention network regions. Across the cerebellum, resting-state functional connectivity with the cortical dorsal attention network strongly predicted the level of activation produced by attention and working memory tasks. Critically, cerebellar voxels that were most strongly connected with the dorsal attention network selectively exhibited load-dependent activity, a hallmark of the neural structures that support visual working memory. Finally, we examined intrinsic functional connectivity between task-responsive portions of cerebellar lobules VIIb/VIIIa and cortex. Cerebellum-to-cortex functional connectivity strongly predicted the pattern of cortical activation during task performance. Moreover, resting-state connectivity patterns revealed that cerebellar lobules VIIb/VIIIa group with cortical nodes of the dorsal attention network. This evidence leads us to conclude that the conceptualization of the dorsal attention network should be expanded to include cerebellar lobules VIIb/VIIIa. SIGNIFICANCE STATEMENT The functional participation of cerebellar structures in nonmotor cortical networks remains poorly understood and is highly understudied, despite the fact that the cerebellum possesses many more neurons than the cerebral cortex. Although visual attention paradigms have been reported to activate cerebellum, many researchers have largely dismissed the possibility of a cerebellar contribution to attention in favor of a motor explanation, namely, eye movements. The present study demonstrates that a cerebellar subdivision (mainly lobules VIIb/VIIIa), which exhibits strong intrinsic functional connectivity with the cortical dorsal attention network, also closely mirrors a myriad of cortical dorsal attention network responses to visual attention and working memory tasks. This evidence strongly supports a reconceptualization of the dorsal attention network to include cerebellar lobules VIIb/VIIIa.
Analgesic, Anti-Inflammatory, and Chondroprotective Activities of Cryptolepis buchanani Extract: In Vitro and In Vivo Studies

Cryptolepis buchanani Roem. & Schult. is widely used in folk medicine in Southeast Asia for treating muscle tension and arthritis. This study aimed to investigate an analgesic activity of the methanol extract of C. buchanani (CBE) in acetic acid-induced writhing response in mice, and to examine its anti-inflammatory activity in ethyl phenylpropiolate- (EPP-) induced ear edema and carrageenan-induced paw edema in rats. Its effects on cartilage degradation induced by interleukin-1β (IL-1β) in porcine cartilage explant culture were also determined. This study demonstrated that CBE significantly reduced acetic acid-induced writhing response. It also inhibited edema formation in both EPP-induced ear edema and carrageenan-induced paw edema models. In cartilage explant culture, CBE significantly reduced the sulfated glycosaminoglycan and hyaluronan released into culture media while it reserved the uronic acid and collagen within the cartilage tissues. It also suppressed the matrix metalloproteinase-2 activity with no effect on cell viability. In conclusion, CBE shows analgesic, anti-inflammatory, and chondroprotective effects in this preliminary study. Therefore, CBE may be useful as an alternative treatment for osteoarthritis.
Association of white matter hyperintensity volume with decreased cognitive functioning: the Framingham Heart Study.

OBJECTIVE To examine the relationship between white matter hyperintensity (WMH) volume on magnetic resonance images and cognitive tests in a large, population-based sample. METHODS Quantitative magnetic resonance imaging and neuropsychological evaluations were performed in 1820 dementia- and stroke-free participants from the Framingham Offspring Cohort. The WMH volume relative to total cranial volume was computed; WMH volumes more than 1 SD above the age-predicted mean were defined as large. Adjusting for age, sex, education, height, and Framingham Stroke Risk Profile, we examined the relationship between WMH and 3 cognitive factors derived from a neuropsychological test battery (verbal memory, visuospatial memory and organization, and visual scanning and motor speed) and 3 individual measures of new learning, abstract reasoning, and naming. RESULTS Compared with those with no or little WMH volume, participants with large WMH volume performed worse on the cognitive factors of visuospatial memory and organization (P = .04) and visual scanning and motor speed (P = .01), as well as on new learning (P = .04), but not on verbal memory (P = .52). CONCLUSIONS In this younger community-based population of nondemented individuals, those with large WMH volume, as compared with those with less or no WMH volumes, performed significantly worse in cognitive domains generally associated with frontal lobe systems and, to a lesser extent, the medial temporal area. Further study will clarify whether large WMH volume and associated cognitive impairment lead to future risk of stroke or dementia.
Effect of Mineralocorticoid Receptor Antagonists on Cardiac Structure and Function in Patients With Diastolic Dysfunction and Heart Failure With Preserved Ejection Fraction: A Meta‐Analysis and Systematic Review

Background There has been an increasing interest in use of mineralocorticoid receptor antagonists (MRAs) in patients with heart failure with preserved ejection fraction (HFPEF). However, a comprehensive evaluation of MRA effects on left ventricular (LV) structure and function in these patients is lacking. In this meta‐analysis, we evaluated the effects of MRAs on LV structure and function among patients with diastolic dysfunction or HFPEF. Methods & Results Randomized, controlled clinical trials evaluating the efficacy of MRAs in patients with diastolic dysfunction or HFPEF were included. The primary outcome was change in E/e’, a specific measure of diastolic function. Secondary outcomes included changes in other measures of diastolic function, LV structure, surrogate markers for myocardial fibrosis (carboxy‐terminal peptide of procollagen type I [PICP] and amino‐terminal peptide of pro‐collagen type‐II [PIIINP]), blood pressure, and exercise tolerance. In the pooled analysis, MRA use was associated with significant reduction in E/e’ (weighted mean difference [WMD] [95% confidence interval {CI}]: −1.68 [−2.03 to −1.33]; P<0.0001) and deceleration time (WMD [95% CI]: −12.0 ms [−23.3 to −0.7]; P=0.04) as compared with control, suggesting and improvement in diastolic function. Furthermore, blood pressure and levels of PIIINP and PICP were also significantly reduced with MRA therapy with no significant change in LV mass or dimensions. Conclusion MRA therapy in patients with asymptomatic diastolic dysfunction or HFPEF is associated with significant improvement in diastolic function and markers of cardiac fibrosis without a significant change in LV mass or dimensions.
Multi-domain transformational design flow for embedded systems

Current tools for embedded system design have limited support for modelling the interaction of the system with its physical environment. Furthermore, the natural representation of (streaming, real-time) applications with dataflow models is not supported by most tools. However, integrating multiple domains supports the design of complex interdisciplinary systems and enables model transformations. In this paper we discuss a unified approach, called UniTi, to handle continuous and discrete time models in a single framework, which includes the dataflow model as well. Our approach consists of a transformational design flow, expressed mathematically in a functional language. We formally distinguish the various domains and explain their interaction. In addition, we give guidelines for specifying algorithms such that these transformations can be applied. Our approach is illustrated with a non-trivial case study: beamforming in a phased array system.
Event Detection using Twitter: A Spatio-Temporal Approach

Background Every day, around 400 million tweets are sent worldwide, which has become a rich source for detecting, monitoring and analysing news stories and special (disaster) events. Existing research within this field follows key words attributed to an event, monitoring temporal changes in word usage. However, this method requires prior knowledge of the event in order to know which words to follow, and does not guarantee that the words chosen will be the most appropriate to monitor. Methods This paper suggests an alternative methodology for event detection using space-time scan statistics (STSS). This technique looks for clusters within the dataset across both space and time, regardless of tweet content. It is expected that clusters of tweets will emerge during spatio-temporally relevant events, as people will tweet more than expected in order to describe the event and spread information. The special event used as a case study is the 2013 London helicopter crash. Results and Conclusion A spatio-temporally significant cluster is found relating to the London helicopter crash. Although the cluster only remains significant for a relatively short time, it is rich in information, such as important key words and photographs. The method also detects other special events such as football matches, as well as train and flight delays from Twitter data. These findings demonstrate that STSS is an effective approach to analysing Twitter data for event detection.
Mycobacterium tuberculosis Modulates miR-106b-5p to Control Cathepsin S Expression Resulting in Higher Pathogen Survival and Poor T-Cell Activation

The success of tuberculosis (TB) bacillus, Mycobacterium tuberculosis (Mtb), relies on the ability to survive in host cells and escape to immune surveillance and activation. We recently demonstrated that Mtb manipulation of host lysosomal cathepsins in macrophages leads to decreased enzymatic activity and pathogen survival. In addition, while searching for microRNAs (miRNAs) involved in posttranscriptional gene regulation during mycobacteria infection of human macrophages, we found that selected miRNAs such as miR-106b-5p were specifically upregulated by pathogenic mycobacteria. Here, we show that miR-106b-5p is actively manipulated by Mtb to ensure its survival in macrophages. Using an in silico prediction approach, we identified miR-106b-5p with a potential binding to the 3′-untranslated region of cathepsin S (CtsS) mRNA. We demonstrated by luminescence-based methods that miR-106b-5p indeed targets CTSS mRNA resulting in protein translation silencing. Moreover, miR-106b-5p gain-of-function experiments lead to a decreased CtsS expression favoring Mtb intracellular survival. By contrast, miR-106b-5p loss-of-function in infected cells was concomitant with increased CtsS expression, with significant intracellular killing of Mtb and T-cell activation. Modulation of miR-106b-5p did not impact necrosis, apoptosis or autophagy arguing that miR-106b-5p directly targeted CtsS expression as a way for Mtb to avoid exposure to degradative enzymes in the endocytic pathway. Altogether, our data suggest that manipulation of miR-106b-5p as a potential target for host-directed therapy for Mtb infection.