Miracle-dz/UniFAR-FTUs huggingface dataset:
Fundamental Groups and Covering Spaces

This introductory textbook describes fundamental groups and their topological soul mates, the covering spaces. The author provides several illustrative examples that touch upon different areas of mathematics, but in keeping with the books introductory aim, they are all quite elementary. Basic concepts are clearly defined, proofs are complete, and no results from the exercises are assumed in the text.
The cis -regulatory of modern human-specific variants.

The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.
Parasitic nematodes—From genomes to control Parasitic nematodes—From genomes to control

The diseases caused by parasitic nematodes in domestic and companion animals are major factors that decrease production and quality of the agricultural products. Methods available for the control of the parasitic nematode infections are mainly based on chemical treatment, non-chemical management practices, immune modulation and biological control. However, even with integrated pest management that frequently combines these approaches, the effective and long-lasting control strategies are hampered by the persistent exposure of host animals to environmental stages of parasites, the incomplete protective response of the host and acquisition of anthelmintic resistance by an increasing number of parasitic nematodes. Therefore, the challenges to improve control of parasitic nematode infections are multi-fold and no single category of information will meet them all. However, new information, such as nematode genomics, functional genomics and proteomics, can strengthen basic and applied biological research aimed to develop improvements. In this review we will, summarize existing control strategies of nematode infections and discuss ongoing developments in nematode genomics. Genomics approaches offer a growing and fundamental base of information, which when coupled with downstream functional genomics and proteomics can accelerate progress towards developing more efﬁcient and sustainable control programs. # 2007 Elsevier B.V. All rights reserved.
The biology and relative abundance of Shortjaw Cisco ( Coregonus zenithicus ) in Lake Nipigon

Shortjaw Cisco ( Coregonus zenithicus ) were originally described in Lake Nipigon in the 1920s, and have been consistently identified in the limited number of subsequent cisco surveys of the lake. With the exception of ecomorphological and genetic research conducted on the cisco community of Lake Nipigon in the late 1990s, little attention has been focused on any cisco species from this lake. DFO Science was charged with conducting a pre-COSEWIC assessment for Shortjaw Cisco, and this manuscript assesses the current: and a limited time Shortjaw Lake Nipigon. The relative abundance of Shortjaw Cisco has declined more than 50% in Lake Nipigon from the 1998-99 through 2008-09 period, and no recent strong year-classes were observed. Mean age of the population is ~12 years, and annual mortality estimates are low (11.7%). The Lake Nipigon Shortjaw Cisco population is dominated by females (sex ratio is 65% female), which appear to have greater longevity than males. Shortjaw Cisco in Lake Nipigon prefer shallower depths (mean depth of capture 30.2 m) than their conspecifics from the Great Lakes. The Shortjaw Cisco population in Lake Nipigon is a Mysis spp. specialist, with the majority of individuals consuming only this prey species. Anthropogenic threats are limited on Lake Nipigon, as only a small fishery is prosecuted on the lake. Observed declines are more likely due to food web changes due to invasive species, or competition with other native fishes.
Current Studies ofthe Folate Antagonists in Patients with Acute Leukemia1

of the folate antagonists in patients with leukemia. Since an extensive review of the niechamiism of action of the folate antagonists in man was presented recently (2), the present paper will not attempt to be exhaustive ; rather, it will di rect attention to certain recent developments. Three areas will be stressed : (a) studies of the enzyme dihydro folate reductase; (b) a discussion of criteria considered im port.amit for responsiveness in patients with acute leukemia treated with methotrexate; and (c) the current status of studies of resistance to the folate antagonists.
The Endoplasmic Reticulum Stress Sensor IRE1 (cid:2) Protects Cells from Apoptosis Induced by the Coronavirus Infectious Bronchitis Virus

The unfolded-protein response (UPR) is a signal transduction cascade triggered by perturbation of the homeostasis of the endoplasmic reticulum (ER). UPR resolves ER stress by activating a cascade of cellular responses, including the induction of molecular chaperones, translational attenuation, ER-associated degradation, and other mechanisms. Under prolonged and irremedia-ble ER stress, however, the UPR can also trigger apoptosis. Here, we report that in cells infected with the avian coronavirus infectious bronchitis virus (IBV), ER stress was induced and the IRE1 (cid:2) -XBP1 pathway of UPR was activated. Knockdown and overexpression experiments demonstrated that IRE1 (cid:2) protects infected cells from IBV-induced apoptosis, which required both its kinase and RNase activities. Our data also suggest that splicing of XBP1 mRNA by IRE1 (cid:2) appears to convert XBP1 from a proapoptotic XBP1u protein to a prosurvival XBP1s protein. Moreover, IRE1 (cid:2) antagonized IBV-induced apoptosis by modulating the phosphorylation status of the proapoptotic c-Jun N-terminal kinase (JNK) and the prosurvival RAC–alpha serine/threo-nine-protein kinase (Akt). Taken together, the data indicate that the ER stress sensor IRE1 (cid:2) is activated in IBV-infected cells and serves as a survival factor during coronavirus infection. well established that the endoplasmic reticulum (ER) is closely associated with coronavirus replication. Here, we report that inositol-requiring protein 1 alpha (IRE1 (cid:2) ), a key sensor of ER stress, is activated in cells infected with the avian coronavirus infectious bronchitis virus (IBV). Moreover, IRE1 (cid:2) is shown to protect the infected cells from apoptosis by modulating the unfolded-protein response (UPR) and two kinases related to cell survival. This study demonstrates that UPR activation constitutes a major aspect of coronavirus-host interactions. Manipula-tions of the coronavirus-induced UPR may provide novel therapeutic targets for the control of coronavirus infection and pathogenesis.
Peptide Nucleic Acid Array for Detection of Point Mutations in Hepatitis B Virus Associated with Antiviral Resistance (cid:1) †

The detection of antiviral-resistant hepatitis B virus (HBV) mutations is important for monitoring the response to treatment and for effective treatment decisions. We have developed an array using peptide nucleic acid (PNA) probes to detect point mutations in HBV associated with antiviral resistance. PNA probes were designed to detect mutations associated with resistance to lamivudine, adefovir, and entecavir. The PNA array assay was sensitive enough to detect 10 2 copies/ml. The PNA array assay was able to detect mutants present in more than 5% of the virus population when the total HBV DNA concentration was greater than 10 4 copies/ml. We analyzed a total of 68 clinical samples by this assay and validated its usefulness by comparing results to those of the sequencing method. The PNA array correctly identiﬁed viral mutants and has high concordance (98.3%) with direct sequencing in detecting antiviral-resistant mutations. Our results showed that the PNA array is a rapid, sensitive, and easily applicable assay for the detection of antiviral-resistant mutation in HBV. Thus, the PNA array is a useful and powerful diagnostic tool for the detection of point mutations or polymorphisms.
Orai1-Mediated I CRAC Is Essential for Neointima Formation After Vascular Injury

Rationale: The molecular correlate of the calcium release-activated calcium current ( I CRAC ), the channel protein Orai1, is upregulated in proliferative vascular smooth muscle cells (VSMC). However, the role of Orai1 in vascular disease remains largely unknown. Objective: The goal of this study was to determine the role of Orai1 in neointima formation after balloon injury of rat carotid arteries and its potential upregulation in a mouse model of VSMC remodeling. Methods and Results: Lentiviral particles encoding short-hairpin RNA (shRNA) targeting either Orai1 (shO-rai1) or STIM1 (shSTIM1) caused knockdown of their respective target mRNA and proteins and abrogated store-operated calcium entry and I CRAC in VSMC; control shRNA was targeted to luciferase (shLuciferase). Balloon injury of rat carotid arteries upregulated protein expression of Orai1, STIM1, and calcium–calmodulin kinase IIdelta2 (CamKII (cid:1) 2); increased proliferation assessed by Ki67 and PCNA and decreased protein expression of myosin heavy chain in medial and neointimal VSMC. Incubation of the injured vessel with shOrai1 prevented Orai1, STIM1, and CamKII (cid:1) 2 upregulation in the media and neointima; inhibited cell proliferation and markedly reduced neointima formation 14 days post injury; similar results were obtained with shSTIM1. VSMC Orai1 and STIM1 knockdown inhibited nuclear factor for activated T-cell (NFAT) nuclear translocation and activity. Furthermore, Orai1 and STIM1 were upregulated in mice carotid arteries subjected to ligation. Conclusions: Orai1 is upregulated in VSMC during vascular injury and is required for NFAT activity, VSMC proliferation, and neointima formation following balloon injury of rat carotids. Orai1 provides a novel target for control of VSMC remodeling during vascular injury or disease. ( Circ Res . 2011;109:534-542.) upregulation is a more general feature of VSMC proliferation in vivo, and neointima formation. ● Orai1 knockdown in VSMC inhibits the nuclear translocation and activity of the transcription factor, nuclear factor for activated T-cells (NFAT). Orai1 and STIM1 are two critical components of the CRAC channel ( I CRAC ) that regulate Ca 2 (cid:1) entry in nonexcitable cells. The role of Orai1 in vascular function and disease is only beginning to emerge. Our work shows that Ca 2 (cid:1) entry through Orai1 and I CRAC is essential for driving VSMC remodeling in vivo during vascular disease such as restenosis. In vivo knockdown of Orai1 by shRNA in a rat balloon injury model prevents upregulation of Orai1, STIM1, and CamKII (cid:3) 2 in VSMC and inhibits VSMC proliferation and neointima formation. Orai1 knockdown in VSMC inhibits NFAT nuclear translocation and activation, providing a potential mechanism for Orai1-dependent regulation of VSMC remodeling. These findings reveal a role for Orai1 and I CRAC in driving VSMC proliferation during vascular disease. Orai1 targeting with specific drugs might have the potential for treatment of vascular occlusive diseases. ,
Carrier transport in 2D graphene layers near the Dirac point

Submitted for the MAR07 Meeting of The American Physical Society Carrier transport in 2D graphene layers near the Dirac point SHAFFIQUE ADAM, E.H. HWANG, S. DAS SARMA, Condensed Matter Theory Center, University of Maryland, College Park, MD 20742-4111, USA — In a recent work we studied carrier transport in gated 2D graphene monolayers theoretically in the presence of scattering by random charged impurity centers using a Boltzmann theory formalism (cond-mat/0610157). Comparing our results with available experimental data suggested that the low density saturation of conductivity arises from charged impurity induced inhomogeneity in the graphene carrier density. In the present work, we develop a model for carrier transport in a disorder-induced inhomogeneous potential and examine the consequences on conductivity. This work was partially supported by U.S. ONR. Shaffique Adam Condensed Matter Theory Center, University of Maryland Date submitted: 21 Nov 2006 Electronic form version 1.4
Lateral force removal of fungal spores to demonstrate how surface properties affect fungal spore retention

Microbial biofouling on polymer surfaces can lead to their biodeterioration. This may result in deterioration of the surface, leading to cracking and fracturing. Fungal spores from Aspergillus niger 1957, Aspergillus niger 1988 and Aureobasidium pullulans were tested to determine their strength of attachment on three surfaces, p(γ-MPS-co-MMA), p(γ-MPS-co-LMA) and spin-coated poly(methyl methacrylate) (PMMAsc), using lateral force measurements. The results demonstrate that A. niger 1957 and A. niger 1988 spores were most easily removed from the p(γ-MPS-co-MMA) surface, which was the surface with the highest Ra value. The A. niger 1957 and A. pullulans spores were most difficult to remove from the PMMAsc surface, which was the hardest surface. A. niger 1988 spores were the most difficult to remove from p(γ-MPS-co-LMA), the most hydrophobic surface. The results with A. pullulans were difficult to elucidate since the spores bound to all three surfaces and were removed with similar rates of force. The lateral force results demonstrate that spore attachment to a surface is a multi-factorial process, and independent surface and microbial factors influence spore binding. Thus, each environmental scenario needs to be considered on an individual basis, since a solution to one biofouling issue will probably not translate across to other systems. This article is part of the theme issue 'Nanocracks in nature and industry'.
Density-functional theory for the crystalline phases of a two-dimensional dipolar Fermi gas

Density-functional theory is utilized to investigate the zero-temperature transition from a Fermi liquid to an inhomogeneous stripe, or Wigner crystal phase, predicted to occur in a one-component, spin-polarized, two-dimensional dipolar Fermi gas. Correlations are treated semi-exactly within the local-density approximation using an empirical fit to Quantum Monte Carlo data. We find that the inclusion of the nonlocal contribution to the Hartree-Fock energy is crucial for the onset of an instability to an inhomogeneous density distribution. Our density-functional theory supports a transition to both a one-dimensional stripe phase, and a triangular Wigner crystal. However, we find that there is an instability first to the stripe phase, followed by a transition to the Wigner crystal at higher coupling.
Research on gear decision method of commercial vehicle based on predictive road information

As an essential part of the transportation industry, it is necessary to reduce the fuel consumption of commercial vehicles from the perspective of the environment and economy. Previous studies have shown that optimizing the gear sequence can reduce vehicle fuel consumption. This paper presents a gear decision method based on predictive road information. Under the model predictive control framework, the dynamic programming algorithm is used to solve the multi-objective optimization problem of gear decision. To solve the problem of the long calculation time of the dynamic programming algorithm, the nonlinear optimization algorithm is used to optimize the dynamic programming sub-problem, and the optimal gear sequence of fuel consumption is obtained. The final optimized gear sequence is obtained through the dynamic programming algorithm. The simulation analysis of the proposed gear shift decision method shows that the gear shift decision method can effectively reduce fuel consumption under fixed working conditions. Compared with the economic shift schedule, the fuel consumption is reduced by 5%, and the computing speed is improved compared with the dynamic programming algorithm.
The statistics of wavelet-based bicoherence

The ability of classical Fourier- and wavelet-based bicoherence to detect phase coupling associated with short-time quadratic nonlinear interactions is compared. The different performance of each bicoherence arises from statistics. Since the wavelet-based bicoherence has a larger number of effective degrees of freedom (dof) than that of Fourier based bicoherence, its significant level of zero-bicoherence has a smaller value. The statistics of wavelet-based zero-level bicoherence is represented empirically for a zero-mean Gaussian random input.
ANALYSIS OF EFFECT OF MATERNAL OBESITY ON MODE OF DELIVERY AND DURATION OF LABOUR IN LOCAL FEMALE POPULATION OF PAKISTAN

: Introduction: Obesity has been designated as one of the most important global health threats worldwide, and its prevalence has been increasing among women of reproductive age. Pregnant ladies constitute a critical subpopulation with a hoisted danger of obesity because of over the top weight pick up. Aims and objectives: The basic aim of the study is to analyze the effect of maternal obesity on mode of delivery and duration of labour in local female population of Pakistan. Material and methods: This study was conducted at CMH Institute of Medical Sciences, Multan during 2017. The data we used for this purpose was secondary data which we obtain from the hospital record. We gathered the data of 200 females from the obstetric records of women with a singleton pregnancy delivering after 24 weeks of gestation. Results: According to the pre-pregnancy BMI, 96 women (11.5%) were underweight, 558 (67.1%) were of normal weight, 134 (16.1%) were overweight and 44 (5.3%) were obese. In addition, birth weight was significantly higher in overweight or obese women than in underweight women (P < 0.05). There were no significant differences between the four pre -pregnancy BMI categories in maternal age, parity, height and gestational week. Conclusion: We concluded that more obese women required IOL and that IOL for these women was associated with increased rates of caesarean section delivery. This relationship also held true
Secure Data Communication Using Internet Of Things

: The rapid growth of the Internet of Things (IoT) has led to a situation where individual manufacturers develop their own communication protocols and frameworks that are often incompatible with other systems. Part of this is due to the use of incompatible communication hardware, and part is due to the entrenched proprietary systems. This has created a heterogeneous communication landscape, where it is difficult for devices to coordinate their efforts. To remedy this, a number of IoT Frameworks have been proposed to provide a common interface between IoT devices. There are many approaches to common frameworks, each with their strengths and weaknesses, but there is no clear winner among them. This proposed work presents a virtual network testbed for implementing smart home IoT Frameworks. The components of various IoT architecture proposals as well as the novel component, the Thing Management System, were combined, consolidated and related to each other to develop the Holistic IoT Architecture Framework. Subsequently, it was shown that the specifications of the architecture framework are suitable to guide the implementation of a prototype.
Role of sodium salicylate in Staphylococcus aureus quorum sensing, virulence, biofilm formation and antimicrobial susceptibility

The widespread threat of antibiotic resistance requires new treatment options. Disrupting bacterial communication, quorum sensing (QS), has the potential to reduce pathogenesis by decreasing bacterial virulence. The aim of this study was to investigate the influence of sodium salicylate (NaSa) on Staphylococcus aureus QS, virulence production and biofilm formation. In S. aureus ATCC 25923 (agr III), with or without serum, NaSa (10 mM) downregulated the agr QS system and decreased the secretion levels of alpha-hemolysin, staphopain A and delta-hemolysin. Inhibition of agr expression caused a downregulation of delta-hemolysin, decreasing biofilm dispersal and increasing biofilm formation on polystyrene and titanium under static conditions. In contrast, NaSa did not increase biofilm biomass under flow but caused one log10 reduction in biofilm viability on polystyrene pegs, resulting in biofilms being twice as susceptible to rifampicin. A concentration-dependent effect of NaSa was further observed, where high concentrations (10 mM) decreased agr expression, while low concentrations (≤0.1 mM) increased agr expression. In S. aureus 8325-4 (agr I), a high concentration of NaSa (10 mM) decreased hla expression, and a low concentration of NaSa (≤1 mM) increased rnaIII and hla expression. The activity of NaSa on biofilm formation was dependent on agr type and material surface. Eight clinical strains isolated from prosthetic joint infection (PJI) or wound infection belonging to each of the four agr types were evaluated. The four PJI S. aureus strains did not change their biofilm phenotype with NaSa on the clinically relevant titanium surface. Half of the wound strains (agr III and IV) did not change the biofilm phenotype in the 3D collagen wound model. In addition, compared to the control, ATCC 25923 biofilms formed with 10 mM NaSa in the collagen model were more susceptible to silver. It is concluded that NaSa can inhibit QS in S. aureus, decreasing the levels of toxin production with certain modulation of biofilm formation. The effect on biofilm formation was dependent on the strain and material surface. It is suggested that the observed NaSa inhibition of bacterial communication is a potential alternative or adjuvant to traditional antibiotics.
Vaccine adjuvants to engage the cross-presentation pathway

Adjuvants are indispensable components of vaccines for stimulating optimal immune responses to non-replicating, inactivated and subunit antigens. Eliciting balanced humoral and T cell-mediated immunity is paramount to defend against diseases caused by complex intracellular pathogens, such as tuberculosis, malaria, and AIDS. However, currently used vaccines elicit strong antibody responses, but poorly stimulate CD8 cytotoxic T lymphocyte (CTL) responses. To elicit potent CTL memory, vaccines need to engage the cross-presentation pathway, and this requirement has been a crucial bottleneck in the development of subunit vaccines that engender effective T cell immunity. In this review, we focus on recent insights into DC cross-presentation and the extent to which clinically relevant vaccine adjuvants, such as aluminum-based nanoparticles, water-in oil emulsion (MF59) adjuvants, saponin-based adjuvants, and Toll-like receptor (TLR) ligands modulate DC cross-presentation efficiency. Further, we discuss the feasibility of using carbomer-based adjuvants as next generation of adjuvant platforms to elicit balanced antibody- and T-cell based immunity. Understanding of the molecular mechanism of DC cross-presentation and the mode of action of adjuvants will pave the way for rational design of vaccines for infectious diseases and cancer that require balanced antibody- and T cell-based immunity.