Miracle-dz/UniFAR-FTUs huggingface dataset:
Primary HIV-1 Infection Is Associated with Preferential Depletion of CD4+ T Lymphocytes from Effector Sites in the Gastrointestinal Tract

Given its population of CCR5-expressing, immunologically activated CD4+ T cells, the gastrointestinal (GI) mucosa is uniquely susceptible to human immunodeficiency virus (HIV)-1 infection. We undertook this study to assess whether a preferential depletion of mucosal CD4+ T cells would be observed in HIV-1–infected subjects during the primary infection period, to examine the anatomic subcompartment from which these cells are depleted, and to examine whether suppressive highly active antiretroviral therapy could result in complete immune reconstitution in the mucosal compartment. Our results demonstrate that a significant and preferential depletion of mucosal CD4+ T cells compared with peripheral blood CD4+ T cells is seen during primary HIV-1 infection. CD4+ T cell loss predominated in the effector subcompartment of the GI mucosa, in distinction to the inductive compartment, where HIV-1 RNA was present. Cross-sectional analysis of a cohort of primary HIV-1 infection subjects showed that although chronic suppression of HIV-1 permits near-complete immune recovery of the peripheral blood CD4+ T cell population, a significantly greater CD4+ T cell loss remains in the GI mucosa, despite up to 5 yr of fully suppressive therapy. Given the importance of the mucosal compartment in HIV-1 pathogenesis, further study to elucidate the significance of the changes observed here is critical.
Time-Dependent Structural Changes of the Dentatothalamic Pathway in Children Treated for Posterior Fossa Tumor

BACKGROUND AND PURPOSE: Injury to the dentatothalamic pathway that originates in the cerebellum has been suggested as a mechanism for neurologic complications in children treated for posterior fossa tumors. We hypothesized that time-dependent changes occur in the dentatothalamic pathway. MATERIALS AND METHODS: Diffusion tensor evaluation was performed in 14 children (median age, 4.1 years; age range, 1–20 years) who underwent serial MR imaging at 3T as part of routine follow-up after posterior fossa tumor resection with or without adjuvant therapy. Tensor metrics were obtained in the acute (≤1 week), subacute (1 to <6 months), and chronic (≥6 months) periods after surgery. We evaluated the following dentatothalamic constituents: bilateral dentate nuclei, cerebellar white matter, and superior cerebellar peduncles. Serial dentate nuclei volumes were also obtained and compared with the patient's baseline. RESULTS: The most significant tensor changes to the superior cerebellar peduncles and cerebellar white matter occurred in the subacute period, regardless of the tumor pathology or therapy regimen, with signs of recovery in the chronic period. However, chronic volume loss and reduced mean diffusivity were observed in the dentate nuclei and did not reverse. This atrophy was associated with radiation therapy and symptoms of ataxia. CONCLUSIONS: Longitudinal diffusion MR imaging in children treated for posterior fossa tumors showed time-dependent tensor changes in components of the dentatothalamic pathway that suggest evolution of structural damage with inflammation and recovery of tissue directionality. However, the dentate nuclei did not show tensor or volumetric recovery, suggesting that the injury may be chronic.
Skeletal Muscle Fiber‐Specific Green Autofluorescence: Potential for Stem Cell Engraftment Artifacts

Adult stem cell research has lately been plagued by controversy regarding the possibility that some adult stem cells can engraft into nonautochthonous tissues. While most reports have observed some level of engraftment, the prevalence has varied in some cases by two orders of magnitude, suggesting that major technical variations may underlie these differences, possibly outweighing the biological basis of the observations. Here we describe bright green autofluorescence in a specific subset of skeletal muscle fibers that strongly resembles emission from green fluorescent protein (GFP). Moreover, we show that oxidative muscle fibers exhibit this autofluorescence, likely due to flavin, associated with NADH dehydrogenase. Finally, we demonstrate that confocal microscopy, in conjunction with spectral scanning, can be used to distinguish between GFP and autofluorescence. We suggest this autofluorescence artifact may account for some of the discrepancies in this field, particularly those describing skeletal muscle engraftment.
Relative bioavailability of copper in tribasic copper chloride to copper in copper sulfate for laying hens based on egg yolk and feather copper concentrations.

This experiment was conducted to determine the relative bioavailability (RBV) of Cu in tribasic copper chloride (TBCC) to Cu in copper sulfate (monohydrate form; CuSO4·H2O) for layer diets based on egg yolk and feather Cu concentrations. A total of 252, 72-wk-old Hy-Line Brown laying hens were allotted to 1 of 7 treatments with 6 replicates consisting of 6 hens per replicate in a completely randomized design. Hens were fed corn-soybean meal-based basal diets supplemented with 0 (basal), 100, 200, or 300 mg/kg Cu from CuSO4 or TBCC for 4 wk. Results indicated that egg production, egg weight, and egg mass were not affected by dietary treatments. However, increasing inclusion levels of Cu in diets from CuSO4 decreased (P < 0.05) feed conversion ratio (FCR), whereas increasing inclusion levels of Cu in diets from TBCC did not affect FCR, indicating significant interaction (P < 0.05). Increasing inclusion levels of Cu from TBCC or CuSO4 increased (P < 0.05) Cu concentrations of egg yolk and feathers. Feather Cu concentrations were greater (P < 0.01) for hens fed diets containing CuSO4 than for hens fed diets containing TBCC. The values for the RBV of Cu in TBCC to Cu in CuSO4 based on log10 transformed egg yolk and feather Cu concentrations were 107.4% and 69.5%, respectively. These values for the RBV of Cu in TBCC did not differ from Cu in CuSO4 (100%). The RBV measured in egg yolk did not differ from the RBV measured in feather. In conclusion, the RBV of Cu in TBCC to Cu in CuSO4 can be determined using Cu concentrations of egg yolk and feathers although the values depend largely on target tissues of laying hens. For a practical application, however, the RBV value of Cu in TBCC to Cu in CuSO4 could be 88.5% when the RBV values determined using egg yolk and feather Cu concentrations were averaged.
Large regional differences in incidence of arthroscopic meniscal procedures in the public and private sector in Denmark

Objectives A recent study reported a large increase in the number of meniscal procedures from 2000 to 2011 in Denmark. We examined the nation-wide distribution of meniscal procedures performed in the private and public sector in Denmark since different incentives may be present and the use of these procedures may differ from region to region. Setting We included data on all patients who underwent an arthroscopic meniscal procedure performed in the public or private sector in Denmark. Participants Data were retrieved from the Danish National Patient Register on patients who underwent arthroscopic meniscus surgery as a primary or secondary procedure in the years 2000 to 2011. Hospital identification codes enabled linkage of performed procedures to specific hospitals. Primary and secondary outcome measures Yearly incidence of meniscal procedures per 100 000 inhabitants was calculated with 95% CIs for public and private procedures for each region. Results Incidence of meniscal procedures increased at private and at public hospitals. The private sector accounted for the largest relative and absolute increase, rising from an incidence of 1 in 2000 to 98 in 2011. In 2011, the incidence of meniscal procedures was three times higher in the Capital Region than in Region Zealand. Conclusions Our study identified a large increase in the use of meniscal procedures in the public and private sector in Denmark. The increase was particularly conspicuous in the private sector as its proportion of procedures performed increased from 1% to 32%. Substantial regional differences were present in the incidence and trend over time of meniscal procedures.
Multigrid with Rough Coefficients and Multiresolution Operator Decomposition from Hierarchical Information Games

We introduce a near-linear complexity (geometric and meshless/algebraic) multigrid/multiresolution method for PDEs with rough ($L^\infty$) coefficients with rigorous a-priori accuracy and performance estimates. The method is discovered through a decision/game theory formulation of the problems of (1) identifying restriction and interpolation operators (2) recovering a signal from incomplete measurements based on norm constraints on its image under a linear operator (3) gambling on the value of the solution of the PDE based on a hierarchy of nested measurements of its solution or source term. The resulting elementary gambles form a hierarchy of (deterministic) basis functions of $H^1_0(\Omega)$ (gamblets) that (1) are orthogonal across subscales/subbands with respect to the scalar product induced by the energy norm of the PDE (2) enable sparse compression of the solution space in $H^1_0(\Omega)$ (3) induce an orthogonal multiresolution operator decomposition. The operating diagram of the multigrid method is that of an inverted pyramid in which gamblets are computed locally (by virtue of their exponential decay), hierarchically (from fine to coarse scales) and the PDE is decomposed into a hierarchy of independent linear systems with uniformly bounded condition numbers. The resulting algorithm is parallelizable both in space (via localization) and in bandwith/subscale (subscales can be computed independently from each other). Although the method is deterministic it has a natural Bayesian interpretation under the measure of probability emerging (as a mixed strategy) from the information game formulation and multiresolution approximations form a martingale with respect to the filtration induced by the hierarchy of nested measurements.
Prototyping of Ubiquitous Music Ecosystems

This paper focuses on the prototyping stage of the design cycle of ubiquitous music ecosystems. The authors present three case studies of prototype deployments for creative musical activities. The first case exemplifies a ubimus system for synchronous musical interaction using a hybrid Java-JavaScript development platform, mow3s-ecolab. The second case study makes use of the HTML5 Web Audio library to implement a loop-based sequencer. The third prototypeâ€”a sine-wave oscillatorâ€”provides an example of using the Chromium open-source sand-boxing technology Portable Native Client (PNaCl) platform for audio programming on the web. This new approach involved porting the Csound language and audio engine to the PNaCl web technology. The PNaCl Csound environment provides programming tools for ubiquitous audio applications that go beyond theWeb Audio framework. The limitations and advantages of the three approaches proposedâ€”the hybrid Java/JavaScript environment, the HTML5 audio library and the PNaCl Csound infrastructureâ€”are discussed in the context of rapid prototyping of ubimus ecosystems.
The Courseware of Discontinuous Nature of Matter in Teaching the States of Matter and Their Changes.

Among three levels of chemical representation, the sub-microscopic level is the most difficult to learn by students. To solve the problem, it is assumed that the concept of the discontinuous nature of matter or particle concept should be mastered initially by students before they learn sub-microscopic representations of further chemical phenomena. 131 junior high school students from two schools participated in this study. The study was carried out by implementing structureoriented chemistry teaching on the particle concept that was assisted by the courseware and was continued by teaching the changing state of matter. The research instruments were written tests, questionnaire, observation sheet and interview guideline. Research data were collected before and after the use of the courseware, as well as before and after the teaching of the changing states of matter. The results show that the use of the courseware increases students’ understanding of the particle concept for both male and female groups. Meanwhile, particle concept only affects the students’ understanding of sub-microscopic representations of the changing states of matter in general and based on gender.
Borrowing from the Crowd: A Study of Recombination in Software Design Competitions

One form of crowdsourcing is the competition, which poses an open call for competing solutions. Commercial systems such as TopCoder have begun to explore the application of competitions to software development, but have important limitations diminishing the potential benefits drawn from the crowd. In particular, they employ a model of independent work that ignores the opportunity for designs to arise from the ideas of multiple designers. In this paper, we examine the potential for software design competitions to incorporate recombination, in which competing designers are given the designs of others and encouraged to use them to revise their own designs. To explore this, we conducted two software design competitions in which participants were asked to produce both an initial and a revised design, drawing on lessons learned from the crowd. We found that, in both competitions, all participants borrowed ideas and most improved the quality of their designs. Our findings demonstrate the potential benefits of recombination in software design and suggest several ways in which software design competitions can be improved.
Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis

Reef-building corals begin as non-calcifying larvae that, upon settling, rapidly begin to accrete skeleton and a protein-rich skeletal organic matrix that attach them to the reef. Here, we characterized the temporal and spatial expression pattern of a suite of biomineralization genes during three stages of larval development in the reef-building coral Pocillopora damicornis: stage I, newly released; stage II, oral-aborally compressed and stage III, settled and calcifying spat. Transcriptome analysis revealed 3882 differentially expressed genes that clustered into four distinctly different patterns of expression change across the three developmental stages. Immunolocalization analysis further reveals the spatial arrangement of coral acid-rich proteins (CARPs) in the overall architecture of the emerging skeleton. These results provide the first analysis of the timing of the biomineralization ‘toolkit’ in the early life history of a stony coral.
Allantoin ameliorates chemically-induced pancreatic β-cell damage through activation of the imidazoline I3 receptors

Objective. Allantoin is the primary active compound in yams (Dioscorea spp.). Recently, allantoin has been demonstrated to activate imidazoline 3 (I3) receptors located in pancreatic tissues. Thus, the present study aimed to investigate the role of allantoin in the effect to improve damage induced in pancreatic β-cells by streptozotocin (STZ) via the I3 receptors. Research Design and Methods. The effect of allantoin on STZ-induced apoptosis in pancreatic β-cells was examined using the ApoTox-Glo triplex assay, live/dead cell double staining assay, flow cytometric analysis, and Western blottings. The potential mechanism was investigated using KU14R: an I3 receptor antagonist, and U73122: a phospholipase C (PLC) inhibitor. The effects of allantoin on serum glucose and insulin secretion were measured in STZ-treated rats. Results. Allantoin attenuated apoptosis and cytotoxicity and increased the viability of STZ-induced β-cells in a dose-dependent manner; this effect was suppressed by KU14R and U73112. Allantoin decreased the level of caspase-3 and increased the level of phosphorylated B-cell lymphoma 2 (Bcl-2) expression detected by Western blotting. The improvement in β-cells viability was confirmed using flow cytometry analysis. Daily injection of allantoin for 8 days in STZ-treated rats significantly lowered plasma glucose and increased plasma insulin levels. This action was inhibited by treatment with KU14R. Conclusion. Allantoin ameliorates the damage of β-cells induced by STZ. The blockade by pharmacological inhibitors indicated that allantoin can activate the I3 receptors through a PLC-related pathway to decrease this damage. Therefore, allantoin and related analogs may be effective in the therapy for β-cell damage.
Unsupervised sub‐segmentation for pigmented skin lesions

Background: Early identification of malignant melanoma with the surgical removal of thin lesions is the most effective treatment for skin cancers. A computer‐aided diagnostic system assists to improve the diagnostic accuracy, where segmenting lesion from normal skin is usually considered as the first step. One of the challenges in the automated segmentation of skin lesions arises from the fact that darker areas within the lesion should be considered separate from the more general suspicious lesion as a whole, because these pigmented areas can provide significant additional diagnostic information.
Pseudomodular surfaces

A Fuchsian group is a discrete subgroup of PSL(2,R). As such it acts discontinuously on H (the upper half plane model of the hyperbolic plane) by fractional linear transformations. This action induces an action on the real line. It is well known that if an isometry of H fixes a point of the real line then the point is one of a pair, in the case that the isometry is hyperbolic or the isometry in question is parabolic and the point in question is unique. Points fixed by parabolic elements of a Fuchsian group Γ shall be referred to as the cusps of Γ. If Γ < PSL(2, k) and k is the smallest such field, then consideration of the equation which must be satisfied by a fixed point shows that a cusp must always lie inside k ∪ {∞}. A classical case where the cusp set is completely understood is the case when Γ = PSL(2,Z), and the cusp set coincides with Q ∪ {∞}. More generally determining the cusp set has been hard to do, with only some moderate success—there is a large literature on this type of problem, see for example [10], [11], [15] and [16] to name a few. Recall that Fuchsian or Kleinian groups Γ1 and Γ2 are commensurable if Γ1 has a subgroup of finite index which is conjugate to a subgroup of finite index in Γ2. This paper is motivated by the following question:
Atmospheric Chemistry and Physics Physical Aerosol Properties and Their Relation to Air Mass Origin at Monte Cimone (italy) during the First Minatroc Campaign

Aerosol physical properties were measured at the Monte Cimone Observatory (Italy) from 1 June till 6 July 2000. The measurement site is located in the transition zone between the continental boundary layer and the free troposphere (FT), at the border between the Mediterranean area and Central Europe, and is exposed to a variety of air masses. Sub-µm number size distributions, aerosol hygro-scopicity near 90% RH, refractory size distribution at 270 • C and equivalent black carbon mass were continuously measured. Number size distributions and hygroscopic properties indicate that the site is exposed to aged continental air masses, however during daytime it is also affected by ups-lope winds. The mixing of this transported polluted boundary layer air masses with relatively clean FT air leads to frequent nucleation events around local noon. Night-time size distributions, including fine and coarse fractions for each air mass episode, have been parameterized by a 3-modal lognormal distribution. Number and volume concentrations in the sub-µm modes are strongly affected by the air mass origin, with highest levels in NW-European air masses, versus very clean, free tropospheric air coming from the N-European sector. During a brief but distinct dust episode, the coarse mode is clearly enhanced. The observed hygroscopic behavior of the aerosol is consistent with the chemical composition described by Putaud et al. (2004), but no closure between known chemical composition and measured hygroscopicity could be made because the hygroscopic properties of the water-soluble organic matter (WSOM) are not known. The data suggest that WSOM is slightly-to-moderately hygroscopic (hygroscopic growth factor GF at 90% relative humidity between 1.05 and 1.51), and that this property may well depend on the air mass origin and history. External mixing of aerosol particles is observed in all air masses through the occurrence of two hygroscopicity modes (average GF of 1.22 and 1.37, respectively). However, the presence of " less " hygroscopic particles has mostly such a low occurrence rate that the average growth factor distribution for each air mass sector actually appears as a single mode. This is not the case for the dust episode, where the external mixing between less hygroscopic and more hygro-scopic particles is very prominent, and indicating clearly the occurrence of a dust accumulation mode, extending down to 50 nm particles, along with an anthropogenic pollution mode. The presented physical measurements finally allow us to provide a partitioning of the sub-µm aerosol in four non-overlapping fractions (soluble/volatile, …
Nature, Position, and Frequency of Mutations Made in a Single Cycle of HIV-1 Replication

ABSTRACT There is considerable HIV-1 variation in patients. The extent of the variation is due to the high rate of viral replication, the high viral load, and the errors made during viral replication. Mutations can arise from errors made either by host DNA-dependent RNA polymerase II or by HIV-1 reverse transcriptase (RT), but the relative contributions of these two enzymes to the mutation rate are unknown. In addition, mutations in RT can affect its fidelity, but the effect of mutations in RT on the nature of the mutations that arise in vivo is poorly understood. We have developed an efficient system, based on existing technology, to analyze the mutations that arise in an HIV-1 vector in a single cycle of replication. A lacZα reporter gene is used to identify viral DNAs that contain mutations which are analyzed by DNA sequencing. The forward mutation rate in this system is 1.4 × 10−5 mutations/bp/cycle, equivalent to the retroviral average. This rate is about 3-fold lower than previously reported for HIV-1 in vivo and is much lower than what has been reported for purified HIV-1 RT in vitro. Although the mutation rate was not affected by the orientation of lacZα, the sites favored for mutations (hot spots) in lacZα depended on which strand of lacZα was present in the viral RNA. The pattern of hot spots seen in lacZα in vivo did not match any of the published data obtained when purified RT was used to copy lacZα in vitro.