Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical management of HIV-associated hematologic malignancies

ABSTRACT HIV is associated with an excess risk for lymphoid malignancies. Although the risk of lymphoma has decreased in HIV-infected individuals in the era of effective combination antiretroviral therapy, it remains high. Treatment outcomes have improved due to improvements in HIV and cancer therapeutics for the common HIV-associated lymphomas. R-CHOP/R-EPOCH are the standard of care for HIV-associated diffuse large B-cell lymphoma. HIV-infected patients with Burkitt lymphoma and good performance status should receive dose-intensive regimens. HIV-infected patients with primary central nervous system lymphoma can respond favorably to high-dose methotrexate-based therapy. In many cases, treatment and expected outcomes for HIV-infected patients with either Hodgkin or non-Hodgkin’s lymphomas are very similar to HIV-negative patients. There is currently no standard treatment for HIV-associated multicentric Castleman disease or primary effusion lymphoma. For those hematologic cancers in which transplantation is part of standard care, this modality should be considered an option in those with well-controlled HIV infection.
Sensorimotor network rewiring in mild cognitive impairment and Alzheimer's disease

This study aimed at elucidating whether (a) brain areas associated with motor function show a change in functional magnetic resonance imaging (fMRI) signal in amnestic mild cognitive impairment (aMCI) and Alzheimer's disease (AD), (b) such change is linear over the course of the disease, and (c) fMRI changes in aMCI and AD are driven by hippocampal atrophy, or, conversely, reflect a nonspecific neuronal network rewiring generically associated to brain tissue damage. FMRI during the performance of a simple motor task with the dominant right‐hand, and structural MRI (i.e., dual‐echo, 3D T1‐weighted, and diffusion tensor [DT] MRI sequences) were acquired from 10 AD patients, 15 aMCI patients, and 11 healthy controls. During the simple‐motor task, aMCI patients had decreased recruitment of the left (L) inferior frontal gyrus compared to controls, while they showed increased recruitment of L postcentral gyrus and head of L caudate nucleus, and decreased activation of the cingulum compared with AD patients. Effective connectivity was altered between primary sensorimotor cortices (SMC) in aMCI patients vs. controls, and between L SMC, head of L caudate nucleus, and cingulum in AD vs. aMCI patients. Altered fMRI activations and connections were correlated with the hippocampal atrophy in aMCI and with the overall GM microstructural damage in AD. Motor‐associated functional cortical changes in aMCI and AD mirror fMRI changes of the cognitive network, suggesting the occurrence of a widespread brain rewiring with increasing structural damage rather than a specific response of cognitive network. Hum Brain Mapp, 2010. © 2009 Wiley‐Liss, Inc.
Comparison of MY09/11 consensus PCR and type-specific PCRs in the detection of oncogenic HPV types

The causal relationship between persistent infection with high‐risk HPV and cervical cancer has resulted in the development of HPV DNA detection systems. The widely used MY09/11 consensus PCR targets a 450bp conserved sequence in the HPV L1 gene, and can therefore amplify a broad spectrum of HPV types. However, limitations of these consensus primers are evident, particularly in regard to the variability in detection sensitivity among different HPV types. This study compared MY09/11 PCR with type‐specific PCRs in the detection of oncogenic HPV types. The study population comprised 15, 774 patients. Consensus PCR failed to detect 522 (10.9%) HPV infections indicated by type‐specific PCRs. A significant correlation between failure of consensus PCR and HPV type was found. HPV types 51, 68 and 45 were missed most frequently. The clinical relevance of the HPV infections missed by MY09/11 PCR was reflected in the fraction of cases with cytological abnormalities and in follow‐up, showing 104 (25.4%) CIN2+ cases. The MY09/11 false negativity could be the result of poor sensitivity, mismatch of MY09/11 primers or disruption of L1 target by HPV integration or DNA degradation. Furthermore, MY09/11 PCR lacked specificity for oncogenic HPVs. Diagnostic accuracy of the PCR systems, in terms of sensitivity (MY09/11 PCR: 87.9%; type‐specific PCRs: 98.3%) and specificity (MY09/11 PCR: 38.7%; type‐specific PCRs: 76.14%), and predictive values for histologically confirmed CIN2+, suggest that type‐specific PCRs could be used in a clinical setting as a reliable screening tool.
Differential effects of egg albumen content on barn swallow nestlings in relation to hatch order

In diverse animal taxa, egg mass variation mediates maternal effects with long‐term consequences for offspring ontogeny and fitness. Patterns of egg mass variation with laying order differ considerably among birds, but no study has experimentally investigated the function of variation in albumen or yolk egg content in the wild. In barn swallows (Hirundo rustica), absolute and relative albumen mass increased with egg laying order. Experimental albumen removal delayed hatching, had larger negative effects on growth of late‐hatched nestlings, and reduced nestling survival. Laying order positively predicted hatch order. Because nestling competitive ability depends on size, and albumen egg content influences hatchling size, present results suggest that by increasing albumen content of late eggs mothers reduce hatching asynchrony and enhance growth particularly of late‐hatched nestlings. Thus, variation in albumen mass with laying order may function to mitigate the negative phenotypic consequences of hatching late in species that adopt a ‘brood‐survival’ strategy.
New model for rigorous analysis of LT-codes

We present a new model for LT codes which simplifies the analysis of the error probability of decoding by belief propagation. For any given degree distribution, we provide the first rigorous expression for the limiting bit-error probability as the length of the code goes to infinity via recent results in random hypergraphs by Darling and Norris, Ann. Appl. Probab. , 2005. For a code of finite length, we provide an algorithm for computing the probability of block-error of the decoder. This algorithm improves by a linear factor the algorithm of Karp, Luby, and Shokrollahi, Proc. of ISIT, 2004
The ER Chaperone LHS1 Is Involved in Asexual Development and Rice Infection by the Blast Fungus Magnaporthe oryzae[C][W][OA]

In planta secretion of fungal pathogen proteins, including effectors destined for the plant cell cytoplasm, is critical for disease progression. However, little is known about the endoplasmic reticulum (ER) secretion mechanisms used by these pathogens. To determine if normal ER function is crucial for fungal pathogenicity, Magnaporthe oryzae genes encoding proteins homologous to yeast Lhs1p and Kar2p, members of the heat shock protein 70 family in Saccharomyces cerevisiae, were cloned and characterized. Like their yeast counterparts, both LHS1 and KAR2 proteins localized in the ER and functioned in an unfolded protein response (UPR) similar to the yeast UPR. Mutants produced by disruption of LHS1 were viable but showed a defect in the translocation of proteins across the ER membrane and reduced activities of extracellular enzymes. The Δlhs1 mutant was severely impaired not only in conidiation, but also in both penetration and biotrophic invasion in susceptible rice (Oryza sativa) plants. This mutant also had defects in the induction of the Pi-ta resistance gene–mediated hypersensitive response and in the accumulation of fluorescently-labeled secreted effector proteins in biotrophic interfacial complexes. Our results suggest that proper processing of secreted proteins, including effectors, by chaperones in the ER is requisite for successful disease development and for determining host-pathogen compatibility via the gene-for-gene interaction.
Differential effects of nitric oxide synthase inhibitors on endotoxin-induced liver damage in rats.

BACKGROUND & AIMS During endotoxemia, expression of inducible nitric oxide synthase (iNOS) and nitric oxide production in the liver is increased. NO has been suggested to have a hepatoprotective function. The aim of this study was to investigate the distribution of iNOS and the effect of different NO synthase inhibitors on liver damage and hemodynamics during endotoxemia. METHODS Rats were injected with lipopolysaccharide (LPS) and received the NOS-inhibitor S-methylisothiourea (SMT) or NG-nitro-L-arginine methyl ester (L-NAME). iNOS induction was assessed by Western blot, immunohistochemistry, and measurement of NO metabolites in plasma and bile. Liver damage was determined by aspartate aminotransferase and alanine aminotransferase and by histology. The effects of both inhibitors on systemic and portal pressure were measured in normal and LPS-treated rats. RESULTS LPS treatment strongly induced iNOS in inflammatory cells, macrophages, bile duct epithelium, and hepatocytes, especially at the canalicular membrane. LPS-induced liver damage strongly increased after L-NAME. SMT caused a similar reduction of NO production without enhancing liver damage. In LPS-treated rats, SMT increased the systemic and portal pressure significantly more than L-NAME. CONCLUSIONS During endotoxemia, administration of the NOS-inhibitor L-NAME aggravates liver damage. This liver damage does not seem to be caused by hemodynamic changes. In contrast, SMT caused significant hemodynamic changes but did not increase LPS-induced liver damage.
Discussion of Relative Price Shocks, Inflation Expectations, and the Role of Monetary Policy

The paper by Pierre Siklos provides a comprehensive overview of developments relevant to inflation expectations (based on survey and non-survey measures of inflation forecasts) in nine economies over the past two decades. In his presentation he made it clear that he would use the terms inflation expectations and inflation forecasts interchangeably. I will mainly use the latter term in this discussion.
Tensile Properties and Swelling Behavior of Sealing Rubber Materials Exposed to High-Pressure Hydrogen Gas

Rubber O-rings exposed to high-pressure hydrogen gas swell, and the volume increase induced by swelling influences tensile properties of the O-rings. Samples of nonfilled (NF), carbon black-filled (CB), and silica-filled (SC) sulfur-vulcanized acrylonitrile-butadiene rubber were exposed to hydrogen at 30 °C and pressures of up to 100 MPa, and the effect of hydrogen exposure on the volume increase, hydrogen content, and tensile properties was investigated. The residual hydrogen content, measured 35 minutes after decompression, increased with increasing hydrogen pressure in the range 0.7–100 MPa for all three samples. In contrast, the volumes of NF, CB, and SC barely changed at pressures below 10 MPa, whereas they increased at pressures above 10 MPa. This nonlinear volume increase is probably related to the free volume of the rubber structure. The volume increase of the CB and SC samples was smaller than that of the NF samples, possibly because of the superior tensile properties of CB and SC. As the volumes of the NF, CB, and SC samples increased, their tensile elastic moduli decreased as a result of a decrease in crosslink density and elongation by volume increase. Although the true fracture stress of NF was barely dependent on the volume of the specimen, those of CB and SC clearly decreased as the volume increased. The decrease in the true fracture stress of CB and SC was related to the volume increase by swelling, showing that the boundary structure between the filler and the rubber matrix was changed by the volume increase.
Cost-utility and cost-effectiveness analyses of a long-term, high-intensity exercise program compared with conventional physical therapy in patients with rheumatoid arthritis.

OBJECTIVE To estimate the cost utility and cost effectiveness of long-term, high-intensity exercise classes compared with usual care in rheumatoid arthritis (RA) patients. METHODS RA patients (n = 300) were randomly assigned to either exercise classes or UC; followup lasted for 2 years. Outcome measures were quality-adjusted life years (QALYs) according to the EuroQol (EQ-5D), Short Form 6D (SF-6D), and a transformed visual analog scale (VAS) rating personal health; functional ability according to the Health Assessment Questionnaire (HAQ) and McMaster Toronto Arthritis Patient Preference Interview (MACTAR); and societal costs. RESULTS QALYs in both randomization groups were similar according to the EQ-5D and SF-6D, but were in favor of usual care according to the VAS (annual difference 0.037 QALY; 95% confidence interval [95% CI] 0.002, 0.069). Functional ability was similar according to the HAQ, but in favor of the exercise classes according to the MACTAR (annual difference 2.9 QALY; 95% CI 0.9, 4.9). Annual medical costs of the exercise program were estimated at 780 per participating patient (1 approximately $1.05). The increase per patient in total medical costs of physical therapy was estimated at 430 (95% CI 318, 577), and the increase in total societal costs at 602 (95% CI -490, 1,664). For societal willingness-to-pay equal to 50,000 per QALY, usual care had better cost utility than exercise classes, and significantly so according to the VAS. CONCLUSION From a societal perspective and without taking possible preventive health effects into account, long-term, high-intensity exercise classes provide insufficient improvement in the valuation of health to justify the additional costs.
The Plastid Casein Kinase 2 Phosphorylates Rubisco Activase at the Thr-78 Site but Is Not Essential for Regulation of Rubisco Activation State

Rubisco activase (RCA) is essential for the activation of Rubisco, the carboxylating enzyme of photosynthesis. In Arabidopsis, RCA is composed of a large RCAα and small RCAβ isoform that are formed by alternative splicing of a single gene (At2g39730). The activity of Rubisco is controlled in response to changes in irradiance by regulation of RCA activity, which is known to involve a redox-sensitive disulfide bond located in the carboxy-terminal extension of the RCAα subunit. Additionally, phosphorylation of RCA threonine-78 (Thr-78) has been reported to occur in the dark suggesting that phosphorylation may also be associated with dark-inactivation of RCA and deactivation of Rubisco. In the present study, we developed site-specific antibodies to monitor phosphorylation of RCA at the Thr-78 site and used non-reducing SDS-PAGE to monitor the redox status of the RCAα subunit. By immunoblotting, phosphorylation of both RCA isoforms occurred at low light and in the dark and feeding peroxide or DTT to leaf segments indicated that redox status of the chloroplast stroma was a critical factor controlling RCA phosphorylation. Use of a knockout mutant identified the plastid-targeted casein kinase 2 (cpCK2α) as the major protein kinase involved in RCA phosphorylation. Studies with recombinant cpCK2α and synthetic peptide substrates identified acidic residues at the –1, +2, and +3 positions surrounding Thr-78 as strong positive recognition elements. The cpck2 knockout mutant had strongly reduced phosphorylation at the Thr-78 site but was similar to wild type plants in terms of induction kinetics of photosynthesis following transfer from darkness or low light to high light, suggesting that if phosphorylation of RCA Thr-78 plays a direct role it would be redundant to redox regulation for control of Rubisco activation state under normal conditions.
Communicating Across Cultures: Social Determinants and Acculturative Consequences

Past research has consistently documented the relations between interethnic contact, language behaviour and identity on the one hand, and the relations between interethnic contact and psychological adjustment on the other. This study combines these two lines of research through a consideration of the influence of ethnolinguistic vitality on these variables' interrelations. The participants included 285 English-Canadian and 243 French-Canadian students at a bilingual university who originated from high and low ethnolinguistic vitality contexts. The results of analyses of variance showed that vitality and native language group membership influenced the extent of ethnic identification, interethnic contact, and self-confidence in the second language, but did not affect the levels of psychological adjustment. Path analyses supported a model in which linguistic self-confidence mediated the relations between interethnic contact and identity and adjustment, although the patterns of relations differed depending upon the vitality of the group. It is suggested that one reason why ethnolinguistic vitality is an important moderator of cross-cultural adaptation is because it implies group differences in the experience of interethnic contact and linguistic self-confidence.
The OxyR Regulon in Nontypeable Haemophilus influenzae

ABSTRACT Nontypeable Haemophilus influenzae (NTHi) is a gram-negative bacterium and a common commensal organism of the upper respiratory tract in humans. NTHi causes a number of diseases, including otitis media, sinusitis, conjunctivitis, exacerbations of chronic obstructive pulmonary disease, and bronchitis. During the course of colonization and infection, NTHi must withstand oxidative stress generated by insult due to multiple reactive oxygen species produced endogenously by other copathogens and by host cells. Using an NTHi-specific microarray containing oligonucleotides representing the 1821 open reading frames of the recently sequenced NTHi isolate 86-028NP, we have identified 40 genes in strain 86-028NP that are upregulated after induction of oxidative stress due to hydrogen peroxide. Further comparisons between the parent and an isogenic oxyR mutant identified a subset of 11 genes that were transcriptionally regulated by OxyR, a global regulator of oxidative stress. Interestingly, hydrogen peroxide induced the OxyR-independent upregulation of expression of the genes encoding components of multiple iron utilization systems. This finding suggested that careful balancing of levels of intracellular iron was important for minimizing the effects of oxidative stress during NTHi colonization and infection and that there are additional regulatory pathways involved in iron utilization.
Microstructure Characterization for Modeling HMA Behaviour using Imaging Technology

ABSTRACT The properties of hot mix asphalt (HMA) highly depend on the microstructure. The ability to experimentally characterize the microstructure is fundamental in describing the macroscopic behavior of HMA. It improves our understanding of the influence of the microstructure distribution on the macroscopic response of the material, which is at the heart of constitutive modeling of granular materials. This paper is an attempt to summarize the recent advances in imaging technology and its applications to the characterization of HMA microstructure including aggregate orientation distribution, aggregate contact, aggregate shape properties, air void distribution, permeability, crack distribution, three-dimensional (3-D) microstructure reconstruction, and microstructure evolution. The microstructure of HMA is linked to the macroscopic behavior of the material within the framework of continuum modeling via microstructure tensors that are incorporated in the continuum modeling formulations. It is envisioned that this link will fill in the gap that has always been present between interpreting laboratory results and the reality of the interior behavior of HMA.
Impact of implementation of a novel antimicrobial stewardship tool on antibiotic use in nursing homes: a prospective cluster randomized control pilot study.

OBJECTIVES To evaluate the impact of 'Resident Antimicrobial Management Plan' (RAMP), a novel antimicrobial stewardship tool on systemic antibiotic use for treatment of infection in nursing homes (NHs). METHODS A pilot cluster randomized control study was conducted in 30 NHs in London. Pre-intervention, we collected point prevalence data on antimicrobial use on three occasions and total antimicrobial consumption for a 12 week period. Post-intervention data were collected in the same manner and included assessment of compliance with RAMP in the intervention group (IG). RESULTS The number of residents included was 1628 pre-intervention [825 IG/803 control group (CG)] and 1610 post-intervention (838 IG/772 CG). The corresponding pre- and post-intervention point prevalence of systemic antibiotic prescribing for treatment of infection was 6.46% and 6.52% in the IG [estimated prevalence ratio: 1.01 (95% CI: 0.81-1.25), P = 0.94] compared with 5.27% and 5.83%, respectively, in the CG [estimated prevalence ratio: 1.11 (95% CI: 0.87-1.41), P = 0.4]. Total antibiotic consumption was 69.78 defined daily doses/1000 residents/day (DRD) pre-intervention and 66.53 DRD post-intervention in the IG compared with 49.68 and 51.92 DRD, respectively, in the CG. There was a significant decrease of 4.9% (3.25 DRD) in the IG (95% CI: 1.0%-8.6%) (P = 0.02) compared with a significant increase of 5.1% (2.24 DRD) in the CG (95% CI: 0.2%-10.2%) (P = 0.04). Main indications for antibiotics were lower respiratory tract infections (34.1%), urinary tract infections (28.5%) and skin/soft tissue infections (25.1%). CONCLUSIONS This pilot study demonstrated that use of RAMP was associated with a statistically significant decrease in total antibiotic consumption and has the potential to be an important antimicrobial stewardship tool for NHs.
Saponin adjuvant induction of ovalbumin-specific CD8+ cytotoxic T lymphocyte responses.

The ability of a saponin adjuvant, QS-21, to induce OVA-specific, class I MHC Ag-restricted CTL was investigated using different forms of soluble OVA and OVA adsorbed onto alum as immunogens. C57BL/6 mice were immunized with soluble native or denatured OVA in formulations that contained increasing quantities of QS-21, and CTL responses were measured using EL4 and E.G7-OVA cells as targets and splenic mononuclear cells as effectors. Ag-specific CTL responses were produced but only if the QS-21 adjuvant was used. Similar responses were induced using alum-adsorbed OVA when mixed with the QS-21 adjuvant but not when used alone. The CTL were specific for an epitope present on the OVA258-276 synthetic peptide, which contains the dominant CTL epitope recognized by C57BL/6 mice. The CD8+ subpopulation of lymphocytes in immune mice was not increased in spleens but increased significantly in vitro after culture with soluble OVA. The CTL activity of splenic mononuclear cell preparations was totally destroyed by treatment with mAb specific to the CD8 Ag plus complement. The ability of the QS-21 adjuvant to induce class I MHC Ag-restricted CTL after immunization with soluble proteins is a characteristic unique to saponin adjuvants.