Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome-wide association study of inflammatory biologic age

Chronic low grade inflammation is a fundamental mechanism of aging. We estimated biologic age using nine biomarkers from diverse inflammatory pathways and we hypothesized that genes associated with inflammatory biological age would provide insights into human aging. In Framingham Offspring Study participants at examination 8 (2005 to 2008), we used the Klemera-Doubal method to estimate inflammatory biologic age and we computed the difference (ΔAge) between biologic age and chronologic age. Gene expression in whole blood was measured using the Affymetrix Human Exon 1.0 ST Array. We used linear mixed effect models to test associations between inflammatory ΔAge and gene expression (dependent variable) adjusting for age, sex, imputed cell counts, and technical covariates. Our study sample included 2386 participants (mean age 67±9 years, 55% women). There were 448 genes significantly were associated with inflammatory ΔAge (P<2.8×10−6), 302 genes were positively associated and 146 genes were negatively associated. Pathway analysis among the identified genes highlighted the NOD-like receptor signaling and ubiquitin mediated proteolysis pathways. In summary, we identified 448 genes that were significantly associated with inflammatory biologic age. Future functional characterization may identify molecular interventions to delay aging and prolong healthspan in older adults.
Anatomical organization of pretectal nuclei and tectal laminae in the cat

Seven nuclei of the pretectum in the cat have been identified and described using material stained for cytoarchitecture and myeloarchitecture, and these have been related to comparable nuclei in other species. These nuclei are termed (1) N. pretectalis anterior, pars compacta and (2) pars reticularis, (3) N. p. medialis, (4) N. p. posterior, (5) N. tractus opticus, (6) N. p. subopticus and (7) N. p. olivaris. Fink‐Heimer stains of terminal degeneration following enucleation indicate that retinopretectal fibers terminate primarily contralaterally in nuclei 4, 5 and 7, and in nuclei 5 and 7 ipsilaterally. At least seven laminae in the superior colliculus have been identified by cytoarchitecture: I. Stratum zonale (two sublayers), II. S. griseum superficiale (three sublayers), III. S. opticum, IV. S. griseum profundum, VII. S. album profundum. The lateral nucleus of the periaqueductal gray might be included as the eighth tectal lamina. Ninety percent or more of the terminal degeneration following enucleation is found on the contralateral side, primarily in the first sublayer of lamina II, with small amounts in the second sublayer; the sparse ipsilateral degeneration is limited to the second sublayer.
Poly(silicate)‐metabolizing silicatein in siliceous spicules and silicasomes of demosponges comprises dual enzymatic activities (silica polymerase and silica esterase)

Siliceous sponges can synthesize poly(silicate) for their spicules enzymatically using silicatein. We found that silicatein exists in silica‐filled cell organelles (silicasomes) that transport the enzyme to the spicules. We show for the first time that recombinant silicatein acts as a silica polymerase and also as a silica esterase. The enzymatic polymerization/polycondensation of silicic acid follows a distinct course. In addition, we show that silicatein cleaves the ester‐like bond in bis(p‐aminophenoxy)‐dimethylsilane. Enzymatic parameters for silica esterase activity are given. The reaction is completely blocked by sodium hexafluorosilicate and E‐64. We consider that the dual function of silicatein (silica polymerase and silica esterase) will be useful for the rational synthesis of structured new silica biomaterials.
Neutrophil Depletion Attenuates Muscle Injury after Exhaustive Exercise.

PURPOSE The infiltration of macrophages in skeletal muscle during exhaustive exercise promotes inflammation, myofiber lesion, and muscle injury. Although neutrophils upregulate macrophage infiltration in skeletal muscles during exercise, the role of neutrophils in promoting muscle injury after exhaustive exercise remains unclear. In this study, we investigated the effects of preexercise neutrophil depletion with antineutrophil antibody treatment on muscle injury, inflammation, and macrophage infiltration after exhaustive exercise. METHODS Male C57BL/6J mice were randomly assigned to four groups, namely, sedentary with control antibody (n = 10), sedentary with antineutrophil antibody (n = 10), exhaustive exercise with control antibody (n = 10), and exhaustive exercise with antineutrophil antibody (n = 10). The mice were given intraperitoneal injection of the antineutrophil antibody (anti-Ly-6G, clone 1A8) or the control antibody (anti-Ly-6G, clone 2A3), and remained inactive or performed exhaustive exercise on a treadmill 48 h after the injection. Twenty-four hours after the exhaustive exercise, the gastrocnemius muscles were removed for histological and polymerase chain reaction (PCR) analyses. Infiltration of neutrophils and macrophages was evaluated with Ly-6G and F4/80 immunohistochemistry staining procedures. Muscle fiber injury was detected based on the number of IgG staining fiber. The mRNA expression levels of proinflammatory cytokines and chemokines were evaluated with real-time reverse transcription PCR. RESULTS Exhaustive exercise increased neutrophil infiltration into the gastrocnemius muscle substantially by 3.1-fold and caused muscle injury, but these effects were markedly suppressed by preexercise treatment with antineutrophil antibody (neutrophil infiltration, 0.42-fold, and muscle injury, 0.18-fold). Treatment with antineutrophil antibody also decreased macrophage infiltration (0.44-fold) and mRNA expression of tumor necrosis factor-α (0.55-fold) and interleukin-6 (0.51-fold) in the skeletal muscle after exhaustive exercise. CONCLUSION These results suggest that neutrophils contribute to exacerbating muscle injury by regulating inflammation through the induction of macrophage infiltration.
A 2.7mW 1MSps 10b analog-to-digital converter with built-in reference buffer and 1LSB accuracy programmable input ranges

A CMOS 1 MSps 10 bit charge-redistribution SAR ADC processes single-ended signals with 1 LSB accuracy selectable input ranges up to supply voltage. A new DAC architecture presents the benefits of a differential approach while sampling single-ended signals. Thanks to new low power design solutions in the ADC comparator and the built-in reference buffer, the total ADC power consumption is only 2.7 mW at 2.4 V supply and 1 MSps. The active area is 0.4 mm/sup 2/ in a 0.35 /spl mu/m CMOS process.
Effects of 14 weeks of progressive endurance training on energy expenditure in elderly people

Effects of progressive endurance training on energy expenditure (EE) were studied in thirteen elderly sedentary subjects (62.8 (sd 2.3) years) after 7 and 14 weeks of training. Daily EE (DEE) and energy cost of the various usual activities were measured over 48 h by whole-body indirect calorimetry. Free-living DEE (DEEFLC) was calculated from 7 d activity recordings and the energy costs of activities were measured in the calorimeters using the factorial method. DEEFLC did not vary significantly throughout the training period despite the additional energy cost of training sessions (0·60 (sd 0·15) MJ/d), because energy expended during free-living activities (EEACT) decreased by 4·8 (sd 7·1) % (P < 0·05) and 7·7 (sd 8·6) % (P < 0·01) after 7 and 14 weeks of training respectively. Measurements in the calorimeters showed that sleeping metabolic rate transiently increased by 4·6 (sd 3·2) % after 7 weeks of training (P < 0·001) and returned to its initial level after 14 weeks of training. BMR was 7·6 (sd 7·0)%(P < 0·01) and 4·1 (sd 6·1)% (P = NS) higher after 7 and 14 weeks of training respectively, than before training. Likewise, diet-induced thermogenesis increased from 3·7 (sd 2·5) to 7·2 (sd 2·8) % energy intake after 7 weeks of training (P < 0·05), and returned to its initial level after 14 weeks of training (4·2 (sd 2·6) % energy intake). Despite these changes, energy expended during activities and the corresponding DEE did not vary throughout the training period. It was concluded that: (1) DEEFLC remained constant throughout the training period due to a compensatory decrease in free-living EEACT; (2) progressive endurance training induced a transient increase in sleeping metabolic rate, BMR and diet-induced thermogenesis after 7 weeks which was not reflected in the energy expended during activities and DEE.
Viewing the antigen‐induced initiation of B‐cell activation in living cells

Summary: The binding of antigen to the B‐cell receptor (BCR) induces BCR clustering and signaling cascades that lead to the activation of a variety of genes associated with B‐cell activation. Over the last several years, our understanding of the molecular details of the BCR signaling pathways have been considerably advanced; what remains only poorly understood are the molecular events that initiate BCR clustering and how clustering leads to activation. Here, we review our progress using live cell imaging technologies to view the earliest events that follow the B cell's binding of antigen. We provide a model for BCR clustering and B‐cell activation that involves an intrinsic tendency of the BCR to cluster and does not require direct crosslinking of the BCR by multivalent antigens. We suggest that local membrane topology and lipid composition play key roles in BCR clustering and initiation of signaling. We believe that our model for B‐cell activation, in which receptor interactions with monovalent antigens on membrane surfaces lead to receptor clustering, may be highly relevant to the mechanisms by which other immune receptors cluster including the T‐cell receptor in response to monovalent peptide–major histocompatibility complex complexes.
Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles.

UNLABELLED Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic. One rare KRAS allele, D33E, displayed tumorigenicity and constitutive activation of known RAS effector pathways. By comparing gene expression changes induced upon expression of wild-type and mutant alleles, we inferred the activity of specific alleles. Because alleles found to be mutated only once in 5,338 tumors rendered cells tumorigenic, these observations underscore the value of integrating genomic information with functional studies. SIGNIFICANCE Experimentally inferring the functional status of cancer-associated mutations facilitates the interpretation of genomic information in cancer. Pooled in vivo screen and gene expression profiling identified functional variants and demonstrated that expression of rare variants induced tumorigenesis. Variant phenotyping through functional studies will facilitate defining key somatic events in cancer. Cancer Discov; 6(7); 714-26. ©2016 AACR.See related commentary by Cho and Collisson, p. 694This article is highlighted in the In This Issue feature, p. 681.
Extracellular Secretion of the Borrelia burgdorferi Oms28 Porin and Bgp, a Glycosaminoglycan Binding Protein

ABSTRACT Borrelia burgdorferi, the Lyme disease pathogen, cycles between its Ixodes tick vector and vertebrate hosts, adapting to vastly different biochemical environments. Spirochete gene expression as a function of temperature, pH, growth phase, and host milieu is well studied, and recent work suggests that regulatory networks are involved. Here, we examine the release of Borrelia burgdorferi strain B31 proteins into conditioned medium. Spirochetes intrinsically radiolabeled at concentrations ranging from 107 to 109 cells per ml secreted Oms28, a previously characterized outer membrane porin, into RPMI medium. As determined by immunoblotting, this secretion was not associated with outer membrane blebs or cytoplasmic contamination. A similar profile of secreted proteins was obtained for spirochetes radiolabeled in mixtures of RPMI medium and serum-free Barbour-Stoenner-Kelly (BSK II) medium. Proteomic liquid chromatography-tandem mass spectrometry analysis of tryptic fragments derived from strain B31 culture supernatants confirmed the identity of the 28-kDa species as Oms28 and revealed a 26-kDa protein as 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase (Pfs-2), previously described as Bgp, a glycosaminoglycan-binding protein. The release of Oms28 into the culture medium is more selective when the spirochetes are in logarithmic phase of growth compared to organisms obtained from stationary phase. As determined by immunoblotting, stationary-phase spirochetes released OspA, OspB, and flagellin. Oms28 secreted by strains B31, HB19, and N40 was also recovered by radioimmunoprecipitation. This is the first report of B. burgdorferi protein secretion into the extracellular environment. The possible roles of Oms28 and Bgp in the host-pathogen interaction are considered.
Discovery of time‐varying relations using fuzzy formal concept analysis and associations

Digital obesity, or information overload, is a widely recognized yet largely unsolved problem. Lack of metadata—that is, a useful and usable description of what is represented by data—is one of the fundamental obstacles preventing the wider use of computational intelligence techniques in tackling the problem of digital obesity. In this paper, we propose the use of fuzzy formal concept analysis to create simple taxonomies, which can be used to structure data and a novel form of fuzzy association rule to extract simple knowledge from data organized hierarchically according to the discovered taxonomies. The association strength is monitored over time, as data sets are updated. Feasibility of the methods is shown by applying them to a large (tens of thousands of entries) database describing reported incidents of terrorism. © 2010 Wiley Periodicals, Inc.
Post-Operative Vision Loss (POVL) following Surgical Procedures

Backgound: Postoperative vision loss (POVL), with a prevalence of 0.1% of cardiopulmonary bypass cases and 0.02% - 0.2% of spine surgery cases, is a rare but devastating complication that can occur in patients undergoing surgery in the prone position. Although the primary cause of this complication is unknown, POVL has been associated with anemia, hypotension (induced or due to hemorrhage), duration of surgery and over hydration. This author reviews the available evidence on the guidelines and management of these patients. Methods: A database search of MEDLINE, Academic Search Complete, Google Scholar, the Cochrane library, PubMed Central, and Embase was done using the key terms and phrases; postoperative vision loss, vision, ischemic optic neuropathy, prone position, perfusion, intraocular pressure, surgery, spinal surgery, scoliosis, blood flow and visual evoked potentials. Non-English language articles were excluded. The majority of the evidence retrieved included case studies, retrospective cohort studies and other literature reviews from dates ranging from 1995-2011. Results: There are no definitive guidelines for the management of patients undergoing spine surgery in the prone position. Conclusion: A synthesis of the literature revealed there is an increased risk of POVL in the presence of both preoperative and intraoperative risk factors. A medical history of diabetes, smoking and vascular disease can all contribute to the development of POVL. Intraoperative risk factors include, but are not limited to, pressure on the orbit, anemia, length of surgery, patient position and amount of volume infused.
Exploring USB Connection Vulnerabilities on Android Devices - Breaches using the Android Debug Bridge

The complexity of avoiding vulnerabilities in the modern mobile operating systems makes them vulnerable to many types of attacks. This paper presents preliminary work in the creation of scenarios to surreptitiously extract private data from smartphones running different versions of the Android Operating System. Three scenarios were already identified and a proof of concept script was developed, all based on the use of the Android Debug Bridge tool. When running in a computer, the script is able to extract private data from a USB connected smartphone. In two scenarios it was possible to extract the information in a totally surreptitious way, without the user knowledge. In the third scenario, using a newer version of the Android operating system, a user action is needed which makes the attack less likely to succeed, but still possible.
LEAD TIME REDUCTION IN AN INTEGRATED INVENTORY MODEL FOR NON-DEFECTIVE ITEMS UNDER A SUPPLY CHAIN SYSTEM

A supply Chain (SC) with single vendor and single buyer is considered. In this research is presents lead time reduction system in an integrated inventory model for non-defective items in order to minimizing the sum of the ordering cost/setup cost, holding cost, transportation cost, production cost and lead time crashing cost of simultaneously optimizing the optimal order quantity, lead time and number of deliveries. The major role of this model is an efficient iterative algorithm has been developed to minimize the integrated total cost for the single vendor and the single buyer integrated system. Furthermore, a numerical example and sensitivity analysis is presented to illustrate the chief issues related to the proposed models. Lead time is a chief part in any inventory management system. In numerous realistic circumstances, lead time can be concentrated by a bonus crashing cost, that is, lead time is controllable. At this point, the buyer lead time can be reduced by paying a bonus crashing cost which is measured as a piecewise linear function. Graphical representation is also presented to illustrate the proposed model. Lastly, a statistical example will be offered to express the integrated inventory model and solution method and provide administrator a useful decision discussion. Sensitivity analyses are used to exemplify the decision-making insights of the model.
K – theory and Exceptional Holonomy in String Theory

In this thesis I consider various aspects of string theory compactifications, especially for nontrivial internal manifolds. The first part is dedicated to the application of K–theory to the study of D–branes. It is the generalized cohomology theory which classifies the possible charges on a given spacetime. A natural question is whether there is any difference between K–theory and the usual description via (de Rahm) cohomology/homology. For this I present a Calabi–Yau manifold which illustrates this difference. Instead of compactifying on a complicated smooth manifold one can also consider orbifolds of simple manifolds to get interesting compactifications. These are described by equivariant K–theory. To be able to compare this with the physical prediction I calculate all KOZ2(R). Furthermore one can consider orientifolds, which suggests the definition of new K–theories. I investigate simple properties of these. In the second part I present compactifications on G2 and Spin(7) manifolds and their description as Gepner models. The SCFT and the geometric description disagree. An explanation for this phenomenon is offered.
Passively pulsed fiber lasers using nanomaterials as saturable absorbers

We demonstrate passively pulsed fiber lasers using two kinds of nanomaterials as saturable absorbers, respectively. Mode-locked optical pulses are achieved by using multilayer molybdenum disulfide (MoS<sub>2</sub>), and Q-switched fiber lasers are realized at 3 μm region by using topological insulator: Bi<sub>2</sub>Te<sub>3</sub>. Experimental proofs are provided.
Ranking of software design alternatives: a fuzzy utility approach

In the software development process, there arises a need for making decision among the alternatives that tries to cover opinion of all decision makers with an attempt to lose minimum possible information. This paper presents an approach to select an optimum software design alternative, considering the opinion of various stakeholders. Importance weights and rating of different criteria as assigned by different decision maker would be used as input to calculate a final utility value associated with respect to usefulness in each alternative involved in strategic decision making process during software development. Based on quality criteria defined by ISO/IEC 9126 model, use of better operators with fuzzy logic is implemented to make less loss of data while calculating utility value. Multi-nomiallogit model would be used to calculate probability of selection of any alternative.
Replication of plasmid-derived human papillomavirus type 11 DNA in cultured keratinocytes

Plasmid-derived human papillomavirus type 11 (HPV11) DNA has been shown to replicate episomally and semiconservatively following transfection of primary human foreskin keratinocytes. HPV11 DNA was excised from the bacterial plasmid, religated to form circular molecules, and cotransfected along with pSV2Neo. Transfectants were selected and shown to contain replicated episomal HPV DNA. Once selected, HPV11 DNA persists in cells through at least two additional passages.
Prevalence of Serotype 19A Streptococcus pneumoniae among Isolates from U.S. Children in 2005-2006 and Activity of Faropenem

ABSTRACT Of 393 isolates of Streptococcus pneumoniae from U.S. children collected in 2005-2006, nonvaccine serotypes accounted for 89.1%, with serotype 19A the most prevalent, representing 30.5% of all isolates. The MIC90 of faropenem against serotype 19A isolates was 1 μg/ml, compared to ≥8 μg/ml against amoxicillin/clavulanate, cefdinir, cefuroxime axetil, and azithromycin.
Evidence for increased susceptibility of Brugia pahangi-infected jirds (Meriones unguiculatus) to subsequent homologous infections

ABSTRACT The effect of existing Brugia pahangi infections on the establishment of a subsequent population was studied using jirds which had pre-challenge infections of 4 and 8 months duration. Necropsies were performed 28 days post-challenge inoculation in order to separate challenge and initial worm populations. The results indicate that existing infections of 4 or 8 months duration increase the susceptibility to subsequent homologous infections. The location of challenge population worms in tissue sites examined did not differ significantly between previously infected and uninfected groups. Previous infections did not affect the early growth of challenge population worms as indicated by their length.
Analysis of the effects of firing rate and synchronization on spike-triggered averaging of neuronal output

Spike-triggered averaging (STA) has been used experimentally to identify multiple features of neuronal output including post-synaptic potentials, whole muscle facilitation, and motor unit output. Using only the most basic assumptions, we develop equations that predict the effects of neuronal firing rate and synchronization on STA. We use exact equations to show that, if the measured neuronal output is multidimensional, then the direction of STA is unaffected by firing rate in the absence of synchronization. We then extend these equations into a framework for analyzing synchronization, and show that under reasonable conditions the analysis of synchronization can be mapped to linear algebra. We consider whether the effects of synchronization can be removed, and if there are neuronal output configurations for which STA is insensitive to synchronization. We conclude that STA can give insight into how neuronal synchronization is organized with respect to neuronal output