Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding Endogenously Formed Communities

A central problem in data mining and social network analysis is determining overlapping communities (clusters) among individuals or objects in the absence of external identification or tagging. We address this problem by introducing a framework that captures the notion of communities or clusters determined by the relative affinities among their members. To this end we define what we call an affinity system, which is a set of elements, each with a vector characterizing its preference for all other elements in the set. We define a natural notion of (potentially overlapping) communities in an affinity system, in which the members of a given community collectively prefer each other to anyone else outside the community. Thus these communities are endogenously formed in the affinity system and are "self-determined" or "self-certified" by its members. We provide a tight polynomial bound on the number of self-determined communities as a function of the robustness of the community. We present a polynomial-time algorithm for enumerating these communities. Moreover, we obtain a local algorithm with a strong stochastic performance guarantee that can find a community in time nearly linear in the of size the community (as opposed to the size of the network). Social networks and social interactions fit particularly naturally within the affinity system framework -- if we can appropriately extract the affinities from the relatively sparse yet rich information from social networks and social interactions, our analysis then yields a set of efficient algorithms for enumerating self-determined communities in social networks. In the context of social networks we also connect our analysis with results about (α, β)-clusters introduced by Mishra, Schreiber, Stanton, and Tarjan [22, 23]. In contrast with the polynomial bound we prove on the number of communities in the affinity system model, we show that there exists a family of networks with superpolynomial number of (α, β)-clusters.
Idiosyncratic development of sensory structures in brains of diapausing butterfly pupae: implications for information processing

Diapause is an important escape mechanism from seasonal stress in many insects. A certain minimum amount of time in diapause is generally needed in order for it to terminate. The mechanisms of time-keeping in diapause are poorly understood, but it can be hypothesized that a well-developed neural system is required. However, because neural tissue is metabolically costly to maintain, there might exist conflicting selective pressures on overall brain development during diapause, on the one hand to save energy and on the other hand to provide reliable information processing during diapause. We performed the first ever investigation of neural development during diapause and non-diapause (direct) development in pupae of the butterfly Pieris napi from a population whose diapause duration is known. The brain grew in size similarly in pupae of both pathways up to 3 days after pupation, when development in the diapause brain was arrested. While development in the brain of direct pupae continued steadily after this point, no further development occurred during diapause until temperatures increased far after diapause termination. Interestingly, sensory structures related to vision were remarkably well developed in pupae from both pathways, in contrast with neuropils related to olfaction, which only developed in direct pupae. The results suggest that a well-developed visual system might be important for normal diapause development.
Darbepoetin‐alfa and intravenous iron administration after autologous hematopoietic stem cell transplantation: A prospective multicenter randomized trial

We conducted a randomized study analyzing the impact of darbepoetin alfa (DA) administration with or without intravenous (i.v.) iron on erythroid recovery after autologous hematopoietic cell transplantation (HCT). Patients were randomized between no DA (Arm 1), DA 300 μg every 2 weeks starting on Day 28 after HCT (Arm 2), or DA plus i.v. iron 200 mg on Days 28, 42, and 56 (Arm 3). The proportion achieving complete hemoglobin (Hb) response within 18 weeks (primary end point) was 21% in Arm 1 (n = 24), 79% in Arm 2 (n = 25), and 100% in Arm 3 (n = 23; P < 0.0001). Erythropoietic response was shown to be significantly higher in Arm 3 (n = 46) than in Arm 2 (n = 50; P = 0.008), resulting in lower DA use, reduced drug costs, and improved quality of life scores, but the effect on transfusions was not significant. In multivariate analysis, DA administration (P < 0.0001), i.v. iron administration (P = 0.0010), high baseline Hb (P < 0.0001), and low baseline creatinine (P = 0.0458) were independently associated with faster achievement of complete Hb response. In conclusion, DA is highly effective to ensure full erythroid reconstitution after autologous HCT when started on Day 28 post‐transplant. I.v. iron sucrose further improves erythroid recovery. Am. J. Hematol. 88:990–996, 2013. © 2013 Wiley Periodicals, Inc.
Reply

To the Editor—We read with great interest the recently published article by Gandra et al that questions the effectiveness of the QuantiFERON-TB Gold In-Tube (QFT-GIT) test (Cellestis) as a screening tool to detect latent tuberculosis infection (LTBI) for healthcare workers (HCWs). We agree with their conclusion that QFT-GIT is not yet completely ready to replace the tuberculin skin test (TST) for screening HCWs in low tuberculosis-incidence countries, considering the high number of positive test results and high reversion rates on repeat testing. Our practical experience with the QFT-GIT test showed similar results and presented challenges very similar to those mentioned in the study by Gandra et al. Annual screening of HCWs for LTBI with TST was the standard infection control practice in our institution (Central Arkansas Veterans Healthcare System, Little Rock, AR) for many years. In November 2008, our hospital replaced the TST with the QFTGIT test for employee testing as well as for screening patients for tuberculosis infection and/or disease. We were confronted with an unexpectedly high number of new converters (more than 20-fold higher than baseline), which led to the dilemma in clinical decision making of whether to offer LTBI treatment since all of these new QFT-GIT converters had a negative TST history. In addition, we encountered high reversion rates (40%) on repeat QFT-GIT testing, similar to the study by Gandra et al, and support the concern about poor shortterm reproducibility of QFT-GIT results in serial testing. Gandra et al raised in their discussion the question of using a higher cutoff value for a positive QFT-GIT test result, given the low prevalence of tuberculosis in the United States. We disagree, however, with raising the cutoff values for a positive test result, for many reasons. There is an overlap among the initial interferon-7 values in HCWs who reverted to negative status and those who retained positive status in our study as well as in the study by Gandra et al. Without a gold standard for the diagnosis of LTBI, it is difficult to differentiate false positive QFT-GIT results from true positive results. To address this problem we suggest adopting a borderline zone between IFN-7 values of 0.35 and 2.0 IU/mL and cautious clinical interpretation of values in this range. Repeat testing with QFT-GIT should be considered for HCWs whose IFN-7 values are in the "borderline" range and whose TST status is negative. However, we do agree completely with Gandra et al that there is a major clinical learning curve ahead to fully unT H E E D I T O R
Theta Dynamics Reveal Domain-specific Control over Stimulus and Response Conflict

Cognitive control allows us to adjust to environmental changes. The medial frontal cortex (MFC) is thought to detect conflicts and recruit additional resources from other brain areas including the lateral prefrontal cortices. Here we investigated how the MFC acts in concert with visual, motor, and lateral prefrontal cortices to support adaptations of goal-directed behavior. Physiologically, these interactions may occur through local and long-range synchronized oscillation dynamics, particularly in the theta range (4–8 Hz). A speeded flanker task allowed us to investigate conflict-type-specific control networks for perceptual and response conflicts. Theta power over MFC was sensitive to both perceptual and response conflict. Interareal theta phase synchrony, however, indicated a selective enhancement specific for response conflicts between MFC and left frontal cortex as well as between MFC and the presumed motor cortex contralateral to the response hand. These findings suggest that MFC theta-band activity is both generally involved in conflict processing and specifically involved in linking a neural network controlling response conflict.
Unlensing Multiple Arcs in 0024+1654: Reconstruction of the Source Image

A unique reconstruction of the image of a high-redshift source galaxy responsible for multiple long arcs in the z = 0.4 cluster 0024+1654 is obtained by inverse lensing. Deep B- and I-band imaging with the Hubble Space Telescope enables high resolution of the arcs due to strong gravitational lensing of the background source. The gravitational lens in the foreground cluster is thus used to obtain a magnified view of the distant source. Four strongly lensed images of the source lead to a unique reconstruction. Each of the long arcs, when unlensed, leads to the same reconstructed source image, exhibiting a beaded, ringlike morphology. The U luminosity of the ring alone is equivalent to that of a normal galaxy. This is likely a galaxy in formation.
Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study

Background Neonatal sepsis in preterm infants is often due to organisms that colonize the skin including Staphylococcus spp. and Candida spp. Development and maturation of the skin microbiome in the neonatal period, especially in preterm infants, may be critical in preventing colonization with pathogens and subsequent progression to neonatal sepsis. Development of the skin microbiome in preterm infants or its determinants in the first 4 weeks of life has not been evaluated. Methods We evaluated the skin microbiome from three body sites, antecubital fossa, forehead and gluteal region, in a prospective cohort of 15 preterm (birth weight < 1500 g and < 32 weeks of gestation) and 15 term neonates. The microbiome community membership and relative abundance were evaluated by amplification and sequencing the bacterial V3-V5 region of the16S rRNA gene on the 454 GS FLX platform. We used linear mixed effects models to analyze longitudinal data. Results The structure and composition of the skin microbiome did not differ between the three sampling sites for term and preterm infants in the neonatal period. However, skin bacterial richness was positively associated with gestational age in the first four weeks of life. Intravenous antibiotics negatively impacted the bacterial diversity of the skin but we did not see differences with respect to feeding or mode of delivery. Conclusions Gestational age, which influences the maturity of skin structure and function, is associated with the development of the preterm cutaneous microbiome. Understanding the maturation of a healthy skin microbiome, prevention of pathogen colonization and its role in the development of immunity will be pivotal in the development of novel interventions to prevent infections in critically ill preterm infants.
Deep venous thrombosis associated with osteomyelitis in children.

BACKGROUND The association of deep venous thrombosis and deep musculoskeletal infection in children has been reported infrequently. The purpose of the present study was to evaluate the characteristics of children with osteomyelitis in whom deep venous thrombosis developed and to compare them with those of children with osteomyelitis in whom deep venous thrombosis did not develop. METHODS A retrospective review of the records of children who were managed at our institution because of a deep musculoskeletal infection between January 2002 and December 2004 identified 212 children with osteomyelitis involving the spine, pelvis, or extremities. Children in whom deep venous thrombosis developed were compared with those in whom it did not develop with respect to age, diagnosis, causative organism, duration of symptoms prior to admission, laboratory values at the time of admission, surgical procedures, and required length of hospitalization. RESULTS Eleven children with osteomyelitis and deep venous thrombosis were identified. The mean C-reactive protein level was 16.9 mg/dL for the group of eleven patients with osteomyelitis in whom deep venous thrombosis developed, compared with only 6.8 mg/dL for the group of 201 patients with osteomyelitis in whom deep venous thrombosis did not develop (p=0.0044). Staphylococcus aureus was the causative organism of infection in all eleven children with deep venous thrombosis and in ninety-three (46%) of the 201 children without deep venous thrombosis. Methicillin-resistant strains of Staphylococcus aureus were identified in eight of the eleven children with deep venous thrombosis and in only forty-nine of the 201 children without deep venous thrombosis. The children with osteomyelitis and deep venous thrombosis were older, had a longer duration of hospitalization, had more admissions to the intensive care unit, and required more surgical procedures than those with osteomyelitis but without deep venous thrombosis. CONCLUSIONS Deep venous thrombosis in association with musculoskeletal infection is more common in children over the age of eight years who have osteomyelitis caused by methicillin-resistant Staphylococcus aureus and who present with a C-reactive protein level of >6 mg/dL. Diagnostic venous imaging studies should be performed to assess for the presence of deep venous thrombosis in children with osteomyelitis, especially those who have these risk factors.
VIB1, a Link between Glucose Signaling and Carbon Catabolite Repression, Is Essential for Plant Cell Wall Degradation by Neurospora crassa

Filamentous fungi that thrive on plant biomass are the major producers of hydrolytic enzymes used to decompose lignocellulose for biofuel production. Although induction of cellulases is regulated at the transcriptional level, how filamentous fungi sense and signal carbon-limited conditions to coordinate cell metabolism and regulate cellulolytic enzyme production is not well characterized. By screening a transcription factor deletion set in the filamentous fungus Neurospora crassa for mutants unable to grow on cellulosic materials, we identified a role for the transcription factor, VIB1, as essential for cellulose utilization. VIB1 does not directly regulate hydrolytic enzyme gene expression or function in cellulosic inducer signaling/processing, but affects the expression level of an essential regulator of hydrolytic enzyme genes, CLR2. Transcriptional profiling of a Δvib-1 mutant suggests that it has an improper expression of genes functioning in metabolism and energy and a deregulation of carbon catabolite repression (CCR). By characterizing new genes, we demonstrate that the transcription factor, COL26, is critical for intracellular glucose sensing/metabolism and plays a role in CCR by negatively regulating cre-1 expression. Deletion of the major player in CCR, cre-1, or a deletion of col-26, did not rescue the growth of Δvib-1 on cellulose. However, the synergistic effect of the Δcre-1; Δcol-26 mutations circumvented the requirement of VIB1 for cellulase gene expression, enzyme secretion and cellulose deconstruction. Our findings support a function of VIB1 in repressing both glucose signaling and CCR under carbon-limited conditions, thus enabling a proper cellular response for plant biomass deconstruction and utilization.
The Effect of Real-World Personal Familiarity on the Speed of Face Information Processing

Background Previous studies have explored the effects of familiarity on various kinds of visual face judgments, yet the role of familiarity in face processing is not fully understood. Across different face judgments and stimulus sets, the data is equivocal as to whether or not familiarity impacts recognition processes. Methodology/Principal Findings Here, we examine the effect of real-world personal familiarity in three simple delayed-match-to-sample tasks in which subjects were required to match faces on the basis of orientation (upright v. inverted), gender and identity. We find that subjects had a significant speed advantage with familiar faces in all three tasks, with large effects for the gender and identity matching tasks. Conclusion/Significance Our data indicates that real-world experience with a face exerts a powerful influence on face processing in tasks where identity information is irrelevant, even in tasks that could in principle be solved via low-level cues. These results underscore the importance of experience in shaping visual recognition processes.
Effects of Intra-Amniotic Lipopolysaccharide and Maternal Betamethasone on Brain Inflammation in Fetal Sheep

Rationale Chorioamnionitis and antenatal glucocorticoids are common exposures for preterm infants and can affect the fetal brain, contributing to cognitive and motor deficits in preterm infants. The effects of antenatal glucocorticoids on the brain in the setting of chorioamnionitis are unknown. We hypothesized that antenatal glucocorticoids would modulate inflammation in the brain and prevent hippocampal and white matter injury after intra-amniotic lipopolysaccharide (LPS) exposure. Methods Time-mated ewes received saline (control), an intra-amniotic injection of 10 mg LPS at 106d GA or 113d GA, maternal intra-muscular betamethasone (0.5 mg/kg maternal weight) alone at 113d GA, betamethasone at 106d GA before LPS or betamethasone at 113d GA after LPS. Animals were delivered at 120d GA (term=150d). Brain structure volumes were measured on T2-weighted MRI images. The subcortical white matter (SCWM), periventricular white matter (PVWM) and hippocampus were analyzed for microglia, astrocytes, apoptosis, proliferation, myelin and pre-synaptic vesicles. Results LPS and/or betamethasone exposure at different time-points during gestation did not alter brain structure volumes on MRI. Betamethasone alone did not alter any of the measurements. Intra-amniotic LPS at 106d or 113d GA induced inflammation as indicated by increased microglial and astrocyte recruitment which was paralleled by increased apoptosis and hypomyelination in the SCWM and decreased synaptophysin density in the hippocampus. Betamethasone before the LPS exposure at 113d GA prevented microglial activation and the decrease in synaptophysin. Betamethasone after LPS exposure increased microglial infiltration and apoptosis. Conclusion Intra-uterine LPS exposure for 7d or 14d before delivery induced inflammation and injury in the fetal white matter and hippocampus. Antenatal glucocorticoids aggravated the inflammatory changes in the brain caused by pre-existing intra-amniotic inflammation. Antenatal glucocorticoids prior to LPS reduced the effects of intra-uterine inflammation on the brain. The timing of glucocorticoid administration in the setting of chorioamnionitis can alter outcomes for the fetal brain.
Silicate weathering in the Himalayas : constraints from the Li isotopic composition of river systems

Chemical weathering of silicate rock consumes atmospheric CO2 and supplies the oceans with cations, thereby controlling both seawater chemistry and climate. The rate of CO2 consumption is closely linked to the rate of CO2 outgassing from the planetary interior, providing a negative feedback loop essential to maintaining an equable climate on Earth. Reconstruction of past global temperatures indicates that a pronounced episode of global cooling began approximately 50 million years ago, coincident with the collision of India and Asia, and the subsequent exhumation of the Himalayas and Tibet. This has drawn attention to the possible links between exhumation, erosion, changes in silicate weathering rates, and climate. However, many of the present-day weathering processes operating on the continents are still debated and remain poorly constrained, hampering our interpretations of marine geochemical archives and past climatic shifts. To constrain the controls on silicate weathering, this thesis investigates the lithium (Li) isotopic composition of river waters, suspended sediments and bed load sediments in the Alaknanda river basin, forming the headwaters of the Ganges. Li almost exclusively reflects silicate weathering, since input from carbonate rocks and biological cycling is minimal. Due to the large fractionation of Li isotopes in the Earth surface environment, Li is sensitive to small changes in silicate weathering processes. The studied rivers show large variations in their Li isotopic composition (δ7Li), ranging from +7.4 to +35.4% , covering much of the observed global riverine variation. These variations are a consequence of the pronounced gradients in climate (rainfall and temperature), and erosion rates across the river basin. This allows a detailed investigation of the controls on Li isotope fractionation, and by extension silicate weathering. The Li isotopic composition of river waters in the Alaknanda basin is modelled using an analytical solution to a one-dimensional reactive transport model. The model incorporates the continuous input of Li from rock dissolution, removal due to secondary mineral formation, and hydrology along subsurface flow paths. Modelling shows that the Li isotopic variations can be described by two dimensionless variables; (1) the Damköhler number, ND, which relates the silicate dissolution rate to the fluid transit time, and (2)
Delphinidin Attenuates Neoplastic Transformation in JB6 Cl41 Mouse Epidermal Cells by Blocking Raf/Mitogen-Activated Protein Kinase Kinase/Extracellular Signal-Regulated Kinase Signaling

Recent studies suggest that anthocyanidins play a pivotal role in the chemopreventive effects of fruits and vegetables. However, the underlying molecular mechanisms and cellular targets remain unknown. Neoplastic transformation of cells and inflammation are considered to be major events contributing to carcinogenesis. Here, we report that delphinidin, a major dietary anthocyanidin, inhibits tumor promoter–induced transformation and cyclooxygenase-2 (COX-2) expression in JB6 promotion-sensitive mouse skin epidermal (JB6 P+) cells by directly targeting Raf and mitogen-activated protein kinase kinase (MEK). Delphinidin inhibited 12-O-tetradecanoylphorbol-13-acetate (TPA)–induced neoplastic transformation and COX-2 expression at both the protein and transcriptional levels. The activation of activator protein-1 and nuclear factor-κB induced by TPA was dose dependently inhibited by delphinidin treatment. Delphinidin strongly suppressed Raf1 and MEK1 kinase activities and subsequently attenuated TPA-induced phosphorylation of MEK, extracellular signal-regulated kinase (ERK), p90RSK, and MSK. Although delphinidin suppressed ERK and c-Jun NH2-terminal kinase activities, it was more effective at inhibiting Raf1 or MEK1 activities. Pull-down and competition assays revealed that delphinidin binds with Raf1 or MEK1 noncompetitively with ATP. Delphinidin also dose dependently suppressed JB6 P+ cell transformation induced by epidermal growth factor and H-Ras, both of which are involved in the activation of Raf/MEK/ERK signaling. Together, these findings suggested that the targeted inhibition of Raf1 and MEK activities and COX-2 expression by delphinidin contribute to the chemopreventive potential of fruits and vegetables.