Miracle-dz/UniFAR-FTUs huggingface dataset:
Leishmania Manipulation of Sand Fly Feeding Behavior Results in Enhanced Transmission

In nature the prevalence of Leishmania infection in whole sand fly populations can be very low (<0.1%), even in areas of endemicity and high transmission. It has long since been assumed that the protozoan parasite Leishmania can manipulate the feeding behavior of its sand fly vector, thus enhancing transmission efficiency, but neither the way in which it does so nor the mechanisms behind such manipulation have been described. A key feature of parasite development in the sand fly gut is the secretion of a gel-like plug composed of filamentous proteophosphoglycan. Using both experimental and natural parasite–sand fly combinations we show that secretion of this gel is accompanied by differentiation of mammal-infective transmission stages. Further, Leishmania infection specifically causes an increase in vector biting persistence on mice (re-feeding after interruption) and also promotes feeding on multiple hosts. Both of these aspects of vector behavior were found to be finely tuned to the differentiation of parasite transmission stages in the sand fly gut. By experimentally accelerating the development rate of the parasites, we showed that Leishmania can optimize its transmission by inducing increased biting persistence only when infective stages are present. This crucial adaptive manipulation resulted in enhanced infection of experimental hosts. Thus, we demonstrate that behavioral manipulation of the infected vector provides a selective advantage to the parasite by significantly increasing transmission.
Portland Cement Concrete Pavement Permeability Performance

The objective of this project was to evaluate the transport properties of concrete pavement in the state of Indiana using common testing procedures. Specifically this work evaluated the absorption of water, the absorption of deicing solutions, and electrical conductivity. A series of concrete paving mixtures were tested to provide a range of values that were typical for the state of Indiana. While similar mixture proportions were used for the mixtures in Indiana differences in the magnitude of water absorbed occurred. A series of mortars were tested to illustrate the effect of curing conditions, water to cement ratio, and paste volume. It was observed that a long duration of drying was needed to obtain equilibrium. Samples dried to a lower relative humidity showed a greater volume of water absorbed. It was observed that drying at 105C resulted in substantial anomalies in water absorption, and as such this method is not recommended. It was observed that when samples were tested using deicing solutions or samples were tested that were previously exposed to deicing solutions the water absorption could be influenced. The electrical conductivity work was performed as a potential method to develop the understanding of rapid test techniques for quality control. The research used a modified parallel law to relate the electrical conductivity to the pore volume, pore solution conductivity and the tortuosity through the pore network. The influence water addition was able to be determined using electrical conductivity. In addition, the pore solution was observed to be approximately linearly related to the degree of hydration. It is critical that a correction be applied to samples tested at different temperatures. An activation energy of conduction was observed that was approximately 10 kiloliters per mole irrespective of water to cement ratio. In addition to the measurement of transport properties, the relative humidity was assessed for concrete exposed to different exposure conditions. The samples considered in this investigation included a sample stored at 50% relative humidity, covered concrete, a concrete with an exposed vertical surface, a concrete on a drainable base, a concrete on a non-drainable base, and concrete that was submerged. The samples showed that for practical field samples the relative humidity in the concrete was always above 80% for the samples tested. The samples that were exposed to precipitation events demonstrated higher relative humidities.
The Primate Lentiviral Receptor Bonzo/STRL33 Is Coordinately Regulated with CCR5 and Its Expression Pattern Is Conserved Between Human and Mouse1

Chemokines play necessary and important roles in regulating the trafficking of lymphocytes to intra- or interlymphoid tissues as well as to sites of inflammation. The complex migratory patterns of lymphoid lineage cells is governed by subset-specific expression of chemokine receptors and their access to specific ligands. Several chemokine receptors and chemokine receptor-like orphan receptors also serve, in conjunction with CD4, as coreceptors for infection by human and simian immunodeficiency viruses (HIV and SIV). Here we show that the expression pattern of Bonzo/STRL33, an orphan SIV/HIV coreceptor, is highly restricted to the memory subset of T cells and is up-regulated upon stimulation of these cells with IL-2 or IL-15. Both the pattern and the regulation of Bonzo expression closely paralleled that of CC family chemokine receptors CCR5 or CCR6 and inversely correlated with CXCR4 expression. However, in striking contrast to CCR5, Bonzo expression was not down-modulated by PMA or mitogen stimulation of T cells. Targeted replacement of the Bonzo gene with a gene encoding green fluorescent protein in mice revealed that the expression and cytokine regulation of mouse Bonzo are comparable to those of its human counterpart. The similar expression and regulation patterns of Bonzo and the HIV coreceptor CCR5 may have implications for understanding the role of HIV/SIV receptors in viral evolution and pathogenesis.
In Vitro and In Vivo Characterization of Anthrax Anti-Protective Antigen and Anti-Lethal Factor Monoclonal Antibodies after Passive Transfer in a Mouse Lethal Toxin Challenge Model To Define Correlates of Immunity

ABSTRACT Passive transfer of antibody may be useful for preexposure prophylaxis against biological agents used as weapons of terror, such as Bacillus anthracis. Studies were performed to evaluate the ability of anthrax antiprotective antigen (anti-PA) and antilethal factor (anti-LF) neutralizing monoclonal antibodies (mAbs) to protect against an anthrax lethal toxin (LeTx) challenge in a mouse model and to identify correlates of immunity to LeTx challenge. Despite having similar affinities for their respective antigens, anti-PA (3F11) and anti-LF (9A11), passive transfer of up to 1.5 mg of anti-PA 3F11 mAb did not provide significant protection when transferred to mice 24 h before LeTx challenge, while passive transfer of as low as 0.375 mg of anti-LF 9A11 did provide significant protection. Serum collected 24 h after passive transfer had LeTx-neutralizing activity when tested using a standard LeTx neutralization assay, but neutralization titers measured using this assay did not correlate with protection against LeTx challenge. However, measurement of LeTx-neutralizing serum responses with an LeTx neutralization assay in vitro employing the addition of LeTx to J774A.1 cells 15 min before the addition of the serum did result in neutralization titers that correlated with protection against LeTx challenge. Our results demonstrate that only the LeTx neutralization titers measured utilizing the addition of LeTx to J774A.1 cells 15 min before the addition of sample correlated with protection in vivo. Thus, this LeTx neutralization assay may be a more biologically relevant neutralization assay to predict the in vivo protective capacity of LeTx-neutralizing antibodies.
Calnexin is associated with and induced by overexpressed human complement protein C2

C2 is a serum glycoprotein that is essential for activation of the classical and lectin pathways of the complement system. We reported previously that in transiently transfected COS cells, C2 accumulates in the endoplasmic reticulum‐Golgi intermediate compartment (ERGIC). Transfection with a cDNA corresponding to a variant C2 mRNA in which exon 17 is spliced out, C2Δ(17), resulted in retention of the mutant polypeptide in the ER. We now show that calnexin, a lectin‐like chaperone, colocalizes with wild‐type (wt) C2 and C2Δ(17). Biosynthetic labeling and sequential immunoprecipitation experiments indicated that colocalization is due to a physical association between calnexin and C2. Immunofluorescence analysis indicated that calnexin was upregulated in cells transfected with either C2 species. Upregulation of calnexin was not affected by castanospermine, which inhibits glucosidases I and II. However, castanospermine inhibited translocation of calnexin to the ERGIC in wt C2 transfected cells. Upregulation of calnexin was also observed in cells transfected with the complement protein factor B, a glycoprotein with extensive structural and functional similarities to C2, but not in cells transfected with complement proteins C3 or factor D, which have no structural similarity to C2, and low or no glycan content, respectively. Calnexin upregulation by transfection with C2 or factor B, but not factor D, was also demonstrated by quantitative analysis of calnexin immunoprecipitates from biosynthetically labeled cells. Increased calnexin expression by overexpressed C2 and factor B appears to be triggered either by the high glycan content of these proteins or, since it also occurs in the presence of castanospermine, by shared features of the structure of these two proteins. Anat Rec 267:7–16, 2002. © 2002 Wiley‐Liss, Inc.
Face image super-resolution via nearest feature line

In this paper, we propose a manifold learning based algorithm using 'Nearest Feature Line - NFL' to hallucinate high-resolution face image. According to the fact that existing NFL can effectively characterize the geometrical proportions to the face samples, we propose using NFL metric to define the neighborhood relations between face samples. Our algorithm can solve the problem that traditional method cannot effectively reveal the similar local geometry between high-resolution and low-resolution face manifolds under the condition that the training sample size is small. Moreover, in order to enhance the representation capacity of available face samples and reduce the computational complexity, we select neighborhood samples for each input LR image. Experimental results demonstrate that our algorithm can generates clearer local feature details, and the PSNR is 1.4 dB higher than that of the best manifold learning based method reported so far.
Educating for empathy. A review.

OBJECTIVE Empathy in the medical setting is appreciation of the patient's emotions and expression of that awareness to the patient. Named as an essential learning objective by the American Association of Medical Colleges, empathy is believed to significantly influence patient satisfaction, adherence to medical recommendations, clinical outcomes, and professional satisfaction. The objective of this study was to identify effective strategies to enhance empathy in undergraduate medical students. DATA SOURCES We searched PubMed for studies that address the effectiveness of strategies for teaching empathy to medical students. We identified 13 peer-reviewed, English language, qualitative and quantitative studies reporting primary data on interventions that aim to foster empathy in undergraduate medical students, using Medical Subject Heading terms education, medical, undergraduate or student, medical crossed with empathy. RESULTS These studies indicate that empathy may be amenable to positive change with a range of interventional strategies. Communication skill workshops addressing the behavioral dimension of empathy show greatest quantitative impact on participants. However, current studies are challenged by varying definitions of empathy, small sample sizes, lack of adequate control groups, and variation among existing empathy measurement instruments. CONCLUSION Given the methodological limitations of the available studies, and uncertainty about which dimensions of empathy should be addressed, larger studies using validated measurement tools are recommended.
Mechanical properties of randomly oriented short Sansevieria trifasciata fibre/epoxy composites

The tensile, flexural and impact properties of randomly oriented short Sansevieria trifasciata fiber/epoxy (STFE) composites were evaluated. Composites were fabricated using raw Sansevieria trifasciata fiber (STFs) with varying lengths (mm) and weight (%) percents of fibers viz. 10(30), 20(35), 30(40) and 40 (45). When the length of the STFs was increased, the tensile, flexural and impact strength properties of the composites were increased up to a 30mm fiber length, and then a curtailment in properties occurred when fiber length further increased. All the fibers were treated with alkali solutionand composites were prepared by hand lay-up method. STFE composites showed a regular trend of an increase in properties with fiber weight percent until 40% and afterwards a decrease in properties of composites with greater fiber weight percent. Tensile tests revealed that the tensile strength was about 75.22 MPa, the Young's modulus was 1.05 GPA and the elongation at the break was 10.07%. The flexural strength and modulus were estimated around 82.33MPa, 3GPa, respectively. Impact tests exhibited strength of approximately 8.97J/cm2. The analysis of the tensile, flexural and impact properties of short STFE composites displayed a critical fiber length and optimum fiber weight percent of 30mm and 40%, respectively. Scanning electron microscope (SEM) studies were carried out to evaluate the fiber/matrix interactions when fiber weight increased. FTIR studies indicated functional groups could engage in the covalent and hydrogen bonds formation. Chemical resistances of the STFE composites were significantly improved for all chemical except for Toluene. These results indicate that high performance all natural products composite materials can be developed from the resources that are readily available locally.
Prevalence of BRCA1 and BRCA2 Germline Mutations in Breast Cancer Women of Multiple Ethnic Region in Northwest China

Purpose The aim of this study is to further understand the status of BRCA1 and BRCA2 mutation among Chinese high-risk breast cancer patients in multiple-ethnic regions of China. Methods A total of 79 blood samples of high-risk breast cancer patients from Xinjiang Uyghur autonomous region were analyzed by PCR-DHPLC sequencing analysis. Results Analysis with full length of the two genes identified a total of 6 deleterious mutations (2073delA, 2394C-T [Q759X] and IVS16+1G>A in BRCA1; 1627A-T [K467X], 6873delCTCC and 9481delA in BRCA2) in this cohort. The prevalence of BRCA1/2 germline mutation was about 7.6% (6/79) in the Xinjiang multiple ethnic region of China. Among them, 3 novel deleterious mutations, 2073delA in BRCA1 (Han ethnic Chinese) and BRCA2 variants 6873delCTCC and 9481delA (both are Kazakh ethnic Chinese), were identified and they had never been reported in breast cancer information core (BIC) database before. 2394C-T (Q759X) and IVS16+1G>A, in BRCA1 and BRCA2 variants 1627A-T were previously reported in other populations but not Chinese. Among 6 of the BRCA-related tumors, three BRCA1- and one BRCA2-associated tumors were in triple negative (estrogen receptor, progesterone receptor, and HER2 negative expressed) status and exhibited a high tumor grade. So far none of these 6 deleterious mutations were reported in ethnic Han Chinese. Conclusion BRCA germline mutation in Chinese multiple ethnicity region may exhibit different genotypes compared to ethnic Han Chinese in other regions. These differences may arise from interaction of genetic background and environmental factors.
Potential Impact of Conjugate Vaccine on the Incidence of Invasive Pneumococcal Disease among Children in Scotland

ABSTRACT We sought to determine the potential impact of seven-valent pneumococcal conjugate vaccine on the incidence of invasive pneumococcal disease (IPD) among children in Scotland. Invasive pneumococci from blood and cerebrospinal fluid, isolated between 2000 and 2004 from all children aged less than 5 years in Scotland, were characterized by serotyping. Using reported efficacy data of the seven-valent pneumococcal conjugate vaccine (PCV7) along with likely coverage rates, we made an estimation of the potential impact on the incidence of IPD among children in Scotland. A total of 217 pneumococci were characterized into 22 different serogroups/types, the most common, in rank order, being 14, 19F, 6B, 18C, 23F, 9V, 4, 1, 19A, and 6A. Estimated serotype coverage for PCV7 was 76.5% in those aged less than 5 years of age but increased to 88.9% for those aged 1 year. By using serotype coverage and estimates of vaccine efficacy and uptake, the potential impact of the vaccine for those greater than 2 months of age, but less than 5 years, was estimated as 67.3%, leading to an average of 29 preventable cases per year. The introduction of PCV7 into the childhood immunization schedule would reduce the burden of pneumococcal disease in children, and the incidence would be particularly reduced in those children aged 1 year. Additional benefits may be gained in adults through herd protection. Continued surveillance of IPD is required before, during, and after the introduction of PCV7.
CacheAudit: A Tool for the Static Analysis of Cache Side Channels

We present CacheAudit, a versatile framework for the automatic, static analysis of cache side channels. CacheAudit takes as input a program binary and a cache configuration and derives formal, quantitative security guarantees for a comprehensive set of side-channel adversaries, namely, those based on observing cache states, traces of hits and misses, and execution times. Our technical contributions include novel abstractions to efficiently compute precise overapproximations of the possible side-channel observations for each of these adversaries. These approximations then yield upper bounds on the amount of information that is revealed. In case studies, we apply CacheAudit to binary executables of algorithms for sorting and encryption, including the AES implementation from the PolarSSL library, and the reference implementations of the finalists of the eSTREAM stream cipher competition. The results we obtain exhibit the influence of cache size, line size, associativity, replacement policy, and coding style on the security of the executables and include the first formal proofs of security for implementations with countermeasures such as preloading and data-independent memory access patterns.
Thymine DNA Glycosylase Is a Positive Regulator of Wnt Signaling in Colorectal Cancer*

Background: Dysregulation of Wnt signaling plays a key role in colorectal cancer (CRC). Results: Thymine DNA glycosylase (TDG) enhances Wnt signaling and is required for CRC growth. Conclusion: TDG is a novel positive regulator in the Wnt pathway and CRC. Significance: TDG could be a novel biomarker and therapeutic target for CRC. Wnt signaling plays an important role in colorectal cancer (CRC). Although the mechanisms of β-catenin degradation have been well studied, the mechanism by which β-catenin activates transcription is still not fully understood. While screening a panel of DNA demethylases, we found that thymine DNA glycosylase (TDG) up-regulated Wnt signaling. TDG interacts with the transcription factor TCF4 and coactivator CREB-binding protein/p300 in the Wnt pathway. Knocking down TDG by shRNAs inhibited the proliferation of CRC cells in vitro and in vivo. In CRC patients, TDG levels were significantly higher in tumor tissues than in the adjacent normal tissues. These results suggest that TDG warrants consideration as a potential biomarker for CRC and as a target for CRC treatment.
Kinetic transport in crystals

One of the central challenges in kinetic theory is the derivation of macroscopic evolution equations--describing, for example, the dynamics of an electron gas--from the underlying fundamental microscopic laws of classical or quantum mechanics. An iconic mathematical model in this research area is the Lorentz gas, which describes an ensemble of non-interacting point particles in an infinite array of spherical scatterers. In the case of a disordered scatterer configuration, the classical results by Gallavotti, Spohn and Boldrighini-Bunimovich-Sinai show that the time evolution of a macroscopic particle cloud is governed, in the limit of small scatterer density (Boltzmann-Grad limit), by the linear Boltzmann equation. In this lecture I will discuss the recent discovery that for a periodic configuration of scatterers the linear Boltzmann equation fails, and the random flight process that emerges in the Boltzmann-Grad limit is substantially more complicated. The key ingredient in the description of the limiting stochastic process is the renormalization dynamics on the space of lattices, a powerful technique that has recently been successfully applied also to other open problems in mathematical physics, including KAM theory and quantum chaos. This lecture is based on joint work with Andreas Strombergsson, Uppsala.
A Compositional Logic for Proving Security Properties of Protocols

We present a logic for proving security properties of protocols that use nonces (randomly generated numbers that uniquely identify a protocol session) and public-key cryptography. The logic, designed around a process calculus with actions for each possible protocol step, consists of axioms about protocol actions and inference rules that yield assertions about protocols composed of multiple steps. Although assertions are written using only steps of the protocol, the logic is sound in a stronger sense: each provable assertion about an action or sequence of actions holds in any run of the protocol that contains the given actions and arbitrary additional actions by a malicious attacker. This approach lets us prove security properties of protocols under attack while reasoning only about the sequence of actions taken by honest parties to the protocol. The main security-specific parts of the proof system are rules for reasoning about the set of messages that could reveal secret data and an invariant ride called the "honesty rule".
BRCA1 in the DNA damage response and at telomeres

Mutations of the breast and ovarian cancer susceptibility gene 1 (BRCA1) account for about 40–45% of hereditary breast cancer cases. Moreover, a significant fraction of sporadic (non-hereditary) breast and ovarian cancers exhibit reduced or absent expression of the BRCA1 protein, suggesting an additional role for BRCA1 in sporadic cancers. BRCA1 follows the classic pattern of a highly penetrant Knudsen-type tumor suppressor gene in which one allele is inactivated through a germ-line mutation and the other is mutated or deleted within the tumor. BRCA1 is a multi-functional protein but it is not fully understood which function(s) is (are) most important for tumor suppression, nor is it clear why BRCA1-mutations confer a high risk for breast and ovarian cancers and not a broad spectrum of tumor types. Here, we will review BRCA1 functions in the DNA damage response (DDR), which are likely to contribute to tumor suppression. In the process, we will highlight some of the controversies and unresolved issues in the field. We will also describe a recently identified and under-investigated role for BRCA1 in the regulation of telomeres and the implications of this role in the DDR and cancer suppression.