Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny and biogeography of dabbling ducks (genus: Anas): A comparison of molecular and morphological evidence

We constructed a phylogeny for the dabbling ducks (tribe Anatini) based on cytochrome-b and ND2 mitochondrial gene DNA sequences. This phylogeny differed in several important respects from a morphological phylogeny developed by Livezey (1991), including the distinctiveness of the blue-winged ducks from other dabbling ducks, the inclusion of the genus Tachyeres and exclusion of Callonetta from the subtribe Anateae, and the lack of support for Mareca as a genus separate from Anas. Characters from three other data sets showed greater consistency with the molecular topology than with the morphological topology. The molecular phylogeny divides the dabbling ducks into four distinct groups: (1) four South American genera, including Amazonetta, Lophonetta, Speculanas, and Tachyeres; (2) the Baikal Teal (Anas formosa); (3) the blue-winged ducks and allies; and (4) a large clade including wigeons, pintails, mallards, and several teal lineages. An examination of the distributions of species in light of the phylogeny indicates relatively little biogeographic structure. Geographic origin for most internal branches is ambiguous using several reconstruction methods. We suggest that the high dispersal ability of birds (especially dabbling ducks) has important implications for recovery of branches using molecular systematics.
"They treated me like a leper". Stigmatization and the quality of life of patients with hepatitis C.

OBJECTIVE Hepatitis C virus is the most prevalent chronic blood-borne infection in the United States, typically acquired through contaminated blood products or needle sharing. We hypothesized that patients with chronic hepatitis C infection experience stigmatization independent of mode of acquisition and that it negatively affects quality of life. DESIGN Cross-sectional observation study. SETTING Specialty clinic in a tertiary referral hospital. PATIENTS Two hundred and ninety outpatients diagnosed with chronic hepatitis C infection and seen in a hepatology clinic. Thirty participants were excluded because of missing data. MEASUREMENTS AND MAIN RESULTS Patients were asked to complete a demographic profile, a semistructured interview, the Sickness Impact Profile, and the Hospital Anxiety Depression Scale. A team of two blinded coders analyzed the interviews. A total of 147 of the 257 study patients experienced stigmatization that they attributed to the disease. Women were more likely to report perceived stigmatization than men (P <.05). Age, education, professional status, and mode of infection did not influence the likelihood of stigmatization. Stigmatization was associated with higher anxiety (P <.01) and depression (P <.01), worsened quality of life (P <.01), loss of control (P <.01), and difficulty coping (P <.01). Individuals who experienced stigmatization also mentioned problems in their health care (P <.01) and work environment (P <.01) as well as with family members (P <.01). CONCLUSION Stigmatization is a very common emotionally burdensome experience for patients with hepatitis C, which can erode social support. As it penetrates even into the health care environment, physicians and other care providers should be aware of the existence and impact of such negative stereotyping.
Combined Biodifferentiating and Antiangiogenic Oral Metronomic Therapy is Feasible and Effective in Relapsed Solid Tumors in Children: Single-Center Pilot Study

To outline an outpatient-based treatment for children with relapsed solid tumors, who already have been extensively pretreated, we defined a 4-drug protocol named COMBAT (combined oral maintenance biodifferentiating and antiangiogenic therapy). Using this protocol, we performed a pilot study to determine its feasibility in children with relapsed and/or high-risk pediatric solid tumors. Patients and Methods: 22 children received the COMBAT protocol. Treatment consisted of daily celecoxib administration along with daily 13-cisretinoic acid (2 weeks on / 2 weeks off) and cycles of metronomic temozolomide (90 mg/m2 for 42 days) and low-dose etoposide (21 days). The treatment was scheduled for a period of 1 year. Results: 9 of the 14 patients assessable for response demonstrated evidence of treatment benefit manifested as prolonged disease stabilization or response. The protocol medication was well tolerated with very good compliance. Only minimal side effects where observed which responded to dose modification or local therapy. Conclusions: The COMBAT regimen is well tolerated by patients with intensive prior therapy including myeloablative regimens. Favorable responses observed in this cohort of patients support the further exploration of this and/or similar strategies in the treatment of pediatric solid tumors.
Faster human activity recognition with SVM

Human activity recognition finds many applications in areas such as surveillance, and sports. Such a system classifies a spatio-temporal feature descriptor of a human figure in a video, based on training examples. However many classifiers face the constraints of the long training time, and the large size of the feature vector. Our method, due to the use of an Support Vector Machine (SVM) classifier, on an existing spatio-temporal feature descriptor resolves these problems in human activity recognition. Comparison of our system with existing classifiers using two standard datasets shows that our system is much superior in terms of the computational time, and either it surpasses or is on par with the existing recognition rates. It performs on par or marginally inferior to existing systems, when the number of training examples are a few due to the imbalance, although consistently better in terms of computation time.
Effects of abscisic acid, ethylene and sugars on the mobilization of storage proteins and carbohydrates in seeds of the tropical tree Sesbania virgata (Leguminosae).

BACKGROUND AND AIMS Endospermic legumes are abundant in tropical forests and their establishment is closely related to the mobilization of cell-wall storage polysaccharides. Endosperm cells also store large numbers of protein bodies that play an important role as a nitrogen reserve in this seed. In this work, a systems approach was adopted to evaluate some of the changes in carbohydrates and hormones during the development of seedlings of the rain forest tree Sesbania virgata during the period of establishment. METHODS Seeds imbibed abscisic acid (ABA), glucose and sucrose in an atmosphere of ethylene, and the effects of these compounds on the protein contents, α-galactosidase activity and endogenous production of ABA and ethylene by the seeds were observed. KEY RESULTS The presence of exogenous ABA retarded the degradation of storage protein in the endosperm and decreased α-galactosidase activity in the same tissue during galactomannan degradation, suggesting that ABA represses enzyme action. On the other hand, exogenous ethylene increased α-galactosidase activity in both the endosperm and testa during galactomannan degradation, suggesting an inducing effect of this hormone on the hydrolytic enzymes. Furthermore, the detection of endogenous ABA and ethylene production during the period of storage mobilization and the changes observed in the production of these endogenous hormones in the presence of glucose and sucrose, suggested a correlation between the signalling pathway of these hormones and the sugars. CONCLUSIONS These findings suggest that ABA, ethylene and sugars play a role in the control of the hydrolytic enzyme activities in seeds of S. virgata, controlling the process of storage degradation. This is thought to ensure a balanced flow of the carbon and nitrogen for seedling development.
Mean field annealing EM for image segmentation

We present a statistical model-based approach to the color image segmentation. A novel deterministic annealing expectation-maximization (EM) and mean field theory are used to estimate the posterior probability of each pixel and the parameters of the Gaussian mixture model which represents the multi-colored objects statistically. Image segmentation is carried out by clustering each pixel into the most probable component Gaussian. The experimental results show that the mean field annealing EM provides a global optimal solution for the maximum likelihood parameter estimation and the real images are segmented efficiently using the estimates computed by the maximum entropy principle and mean field theory.
The Need for a Theory of citing

Metaphorically speaking, citations are frozen footprints in the landscape of scholarly achievement; footprints which bear witness to the passage of ideas. From footprints it is possible to deduce direction; from the configuration and depth of the imprint it should be possible to construct a picture of those who have passed by, whilst the distribution and variety furnish clues as to whether the advance was orderly and purposive. So it is with citations in respect of the growth of human knowledge; they give substantive expression to the process of innovation, and, if properly marshalled, can provide the researcher with a forensic tool of seductive power and versatility.
Fentanyl buccal tablet: rapid relief from breakthrough pain

Breakthrough pain – a transient increase in pain occurring over a baseline of controlled persistent pain – represents an important clinical challenge in the management of cancer and other chronic pain conditions. The fentanyl buccal tablet is a new sugar-free, easily-administered formulation that uses an effervescent drug delivery system to enhance the rate and extent of fentanyl absorption across the buccal mucosa. Clinical trials indicate that the rapid systemic exposure provided by fentanyl buccal tablets translates into clinically significant improvements in pain intensity. Pain relief is observed within 10 – 15 min of administration. Fentanyl buccal tablets are generally well tolerated, with the most commonly observed adverse events being typical opioid side effects. Fentanyl buccal tablets represent a convenient and effective treatment for the control of breakthrough pain.
Prospective RBC phenotype matching in a stroke‐prevention trial in sickle cell anemia: a multicenter transfusion trial

BACKGROUND: Most sickle cell anemia patients undergo transfusion therapy to prevent complications. The Stroke Prevention Trial in Sickle Cell Anemia showed that transfusion therapy is effective in the primary prevention of stroke. Despite its efficacy, transfusion therapy is limited by alloimmunization. The purpose of this study was to determine if a multicenter trial could implement a transfusion program utilizing phenotypically matched blood to reduce alloimmunization.
The Impact of Cognitive Stressors in the Emergency Department on Physician Implicit Racial Bias.

OBJECTIVES The emergency department (ED) is characterized by stressors (e.g., fatigue, stress, time pressure, and complex decision-making) that can pose challenges to delivering high-quality, equitable care. Although it has been suggested that characteristics of the ED may exacerbate reliance on cognitive heuristics, no research has directly investigated whether stressors in the ED impact physician racial bias, a common heuristic. We seek to determine if physicians have different levels of implicit racial bias post-ED shift versus preshift and to examine associations between demographics and cognitive stressors with bias. METHODS This repeated-measures study of resident physicians in a pediatric ED used electronic pre- and postshift assessments of implicit racial bias, demographics, and cognitive stressors. Implicit bias was measured using the Race Implicit Association Test (IAT). Linear regression models compared differences in IAT scores pre- to postshift and determined associations between participant demographics and cognitive stressors with postshift IAT and pre- to postshift difference scores. RESULTS Participants (n = 91) displayed moderate prowhite/antiblack bias on preshift (mean ± SD = 0.50 ± 0.34, d = 1.48) and postshift (mean ± SD = 0.55 ± 0.39, d = 1.40) IAT scores. Overall, IAT scores did not differ preshift to postshift (mean increase = 0.05, 95% CI = -0.02 to 0.14, d = 0.13). Subanalyses revealed increased pre- to postshift bias among participants working when the ED was more overcrowded (mean increase = 0.09, 95% CI = 0.01 to 0.17, d = 0.24) and among those caring for >10 patients (mean increase = 0.17, 95% CI = 0.05 to 0.27, d = 0.47). Residents' demographics (including specialty), fatigue, busyness, stressfulness, and number of shifts were not associated with postshift IAT or difference scores. In multivariable models, ED overcrowding was associated with greater postshift bias (coefficient = 0.11 per 1 unit of NEDOCS score, SE = 0.05, 95% CI = 0.00 to 0.21). CONCLUSIONS While resident implicit bias remained stable overall preshift to postshift, cognitive stressors (overcrowding and patient load) were associated with increased implicit bias. Physicians in the ED should be aware of how cognitive stressors may exacerbate implicit racial bias.
Regulation of MAPK/ERK phosphorylation via ionotropic glutamate receptors in cultured rat striatal neurons

Extracellular signals may regulate mitogen‐activated protein kinase (MAPK) cascades through a receptor‐mediated mechanism. As a signaling superhighway to the nucleus, active Ras‐MAPK cascades phosphorylate transcription factors and facilitate gene expression. In cultured rat striatal neurons, the present work systemically examined the linkage between glutamate receptors and the extracellular signal‐regulated kinase 1/2 (ERK1/2) subclass of MAPK. We found that glutamate induced a rapid and transient phosphorylation of ERK1/2. Similar responses of ERK1/2 phosphorylation were also induced by the ligands selective for each of three subtypes of ionotropic receptors (NMDA, AMPA and kainate), although not by the subgroup‐selective agonists for three subgroups of metabotropic glutamate receptors after 8–9 days in culture. The ERK1/2 phosphorylation induced by all ionotropic receptor agents was dose‐, time‐ and Ca2+ influx‐dependent and occurred in neurons, but not glia. The NMDA‐, AMPA‐ and kainate‐induced ERK1/2 phosphorylation was blocked only by the antagonists selective for respective subtypes. The ERK1/2 phosphorylation induced by these agents was also sensitive to the MAPK kinase 1 (MEK1) inhibitor PD98059 and the MEK1/2 inhibitor U0126. In a further attempt to evaluate the role of active ERK1/2 in activating a downstream transcription factor cAMP response element‐binding protein (CREB), NMDA, AMPA, and kainate were found to increase CREB phosphorylation. The NMDA‐ and AMPA/kainate‐induced CREB phosphorylation was completely and partially blocked by U0126, respectively. These results revealed a positive linkage between ionotropic glutamate receptors and MEK‐sensitive ERK1/2 phosphorylation in striatal neurons. The active ERK1/2 cascade activates the downstream transcription factor CREB to participate in the regulation of gene expression.
CHIP participates in protein triage decisions by preferentially ubiquitinating Hsp70‐bound substrates

The E3 ubiquitin ligase CHIP (C‐terminus of Hsc70‐interacting protein) is believed to be a central player in the cellular triage decision, as it links the molecular chaperones Hsp70/Hsc70 and Hsp90 to the ubiquitin proteasomal degradation pathway. To better understand the decision process, we determined the affinity of CHIP for Hsp70 and Hsp90 using isothermal titration calorimetry. We analyzed the influence of CHIP on the ATPase cycles of both chaperones in the presence of co‐chaperones and a substrate, and determined the ubiquitination efficacy of CHIP in the presence of the chaperones. We found that CHIP has a sixfold higher affinity for Hsp90 compared with Hsc70. CHIP had no influence on ADP dissociation or ATP association, but reduced the Hsp70 cochaperone Hdj1‐stimulated single‐turnover ATPase rates of Hsc70 and Hsp70. CHIP did not influence the ATPase cycle of Hsp90 in the absence of co‐chaperones or in the presence of the Hsp90 cochaperones Aha1 or p23. Polyubiquitination of heat‐denatured luciferase and the native substrate p53 was much more efficient in the presence of Hsc70 and Hdj1 than in the presence of Hsp90, indicating that CHIP preferentially ubiquitinates Hsp70‐bound substrates.
The C3435T mutation in the human MDR1 gene is associated with altered efflux of the P-glycoprotein substrate rhodamine 123 from CD56+ natural killer cells.

P-glycoprotein (PGP) is a membrane protein which determines drug disposition in humans (e.g. digoxin). It is also expressed in various leukocyte lineages with highest expression in CD56+ natural killer cells. Recently, a polymorphism in exon 26 (C3435T) of this gene was shown to correlate with intestinal PGP expression and function in humans. Carriers homozygous for this polymorphism (TT) showed more than two-fold lower PGP expression and higher digoxin plasma concentrations compared to the CC group. However, it is not known whether this mutation in the MDR1 gene is also associated with altered PGP function in peripheral blood cells. We therefore assessed efflux of the PGP-substrate rhodamine 123 from CD56+ natural killer cells. Leukocytes were isolated from whole blood of 10 CC, 10 CT and 11 TT healthy Caucasian individuals. Using flow cytometry, rhodamine fluorescence was determined in CD56+ cells. Moreover, MDRI mRNA was quantified in leukocytes by real-time polymerase chain reaction. Subjects with CC genotype revealed a significantly lower rhodamine fluorescence (i.e. higher PGP function) compared to individuals with TT genotype (51.1 +/- 11.4% versus 67.5 +/- 9.5%, p < 0.01). Heterozygous individuals had an intermediate rhodamine fluorescence (61.4 +/- 6.3%). MDR1 mRNA normalized for cyclophilin was lowest in the TT population (1.29 +/- 1.01), intermediate in heterozygous subjects (1.60 +/- 0.76) and highest in the CC group (1.91 +/- 0.94; not significant). In summary, subjects being homozygous for C in position 3435 of the MDR1 gene have a more pronounced efflux of rhodamine from CD56+ natural killer cells and a higher MDR1 mRNA expression in leukocytes than subjects with the TT genotype. Measurement of rhodamine efflux using flow-cytometry from peripheral blood cells allows assessment of genetically determined differences in P-glycoprotein function.
Defective accessory genes in a human immunodeficiency virus type 1-infected long-term survivor lacking recoverable virus

We have been studying a patient who acquired human immunodeficiency virus (HIV) infection via a blood transfusion 13 years ago. She has remained asymptomatic since that time. The blood donor and two other recipients have all died of AIDS. Although this patient has shown persistently strong seroreactivity to HIV type 1 (HIV-1) antigens by Western blot (immunoblot), she has been continually HIV culture negative in results from multiple laboratories over the last 6 years and has a very low viral burden. Her CD4+ T-cell count has fluctuated around a mean of 399 cells per microliters, with little change in lymphocyte subset percentages. Strong cellular immune responses to HIV-1 epitopes by this patient have been demonstrated. We now report the results of an intensive molecular genetic analysis of the HIV-1 proviral quasispecies from this patient sampled over 5 years. Long terminal repeat region sequences supported the argument for normal basal and Tat-mediated promoter activities. Sequential sequencing of the nef gene revealed a low frequency (8.3%) of defective genes and a striking lack of sequence evolution. Functional analysis of predominant nef genes by both a cell surface CD4 downregulation and a viral infectivity complementation assay showed wild-type function. In contrast, sequential analysis of an amplicon containing the vif, vpr, vpu, tat1, and rev1 genes revealed the presence of inactivating mutations in 64% of the clones. These data suggest that this patient, initially infected with a virulent swarm of HIV-1, is presently infected with a more-attenuated viral quasispecies as a result of effective host immunity.
Mutations in components of the Wnt signaling pathway in gastric cancer.

AIM To explore the contribution of AXIN1, AXIN2 and beta-catenin, components of Wnt signaling pathway, to the carcinogenesis of gastric cancer (GC), we examined AXIN1, AXIN2 exon7 and CTNNB1 (encoding beta-catenin) exon3 mutations in 70 GCs. METHODS The presence of mutations was identified by polymerase chain reaction (PCR)-based denaturing high-performance liquid chromatography and direct DNA sequencing. Beta-catenin expression was detected by immunohistochemical analysis. RESULTS Among the 70 GCs, 5 (7.1%) had mutations in one or two of these three components. A frameshift mutation (1 bp deletion) in exon7 of AXIN2 was found in one case. Four cases, including the case with a mutation in AXIN2, had frameshift mutations and missense mutations in AXIN1. Five single nucleotide polymorphisms (SNPs), 334 C>T, 874 C>T, 1396 G>A, 1690 C>T and 1942 T>G, were identified in AXIN1. A frameshift mutation (27 bp deletion) spanning exon3 of CTNNB1 was observed in one case. All four cases with mutations in AXIN1 and AXIN2 showed nuclear beta-catenin expression. CONCLUSION These data indicate that the mutations in AXIN1 and AXIN2 may contribute to gastric carcino-genesis.
Integration of high-performance SiGe:C HBTs with thin-film SOI CMOS

A new scheme for the integration of high-performance HBTs with thin-film SOI CMOS is demonstrated. The thickness incompatibility problem of thin-body SOI CMOS and high-performance SiGe HBTs is solved by forming HBTs on silicon islands in the BOX. Low-resistance collector wells are realized by ion implantation into the SOI substrate. SiGe:C HBTs with f/sub T//f/sub max/ values of 220 GHz/230 GHz and a BV/sub CEO/ of 2.0 V and fully-depleted CMOS transistors with 90 nm gate length are fabricated on SOI wafers with 30 nm Si thickness.
Influence of Cold Water Immersion on Limb and Cutaneous Blood Flow at Rest

Background: Cold water immersion reduces exercise-induced muscle damage. Benefits may partly arise from a decline in limb blood flow; however, no study has comprehensively investigated the influence of different degrees of cooling undertaken via cold water immersion on limb blood flow responses. Purpose: To determine the influence of cold (8°C) and cool (22°C) water immersion on lower limb and cutaneous blood flow. Study Design: Controlled laboratory study. Methods: Nine men were placed in a semireclined position and lowered into 8°C or 22°C water to the iliac crest for two 5-minute periods interspersed with 2 minutes of nonimmersion. Rectal and thigh skin temperature, deep and superficial muscle temperature, heart rate, mean arterial pressure, thigh cutaneous blood velocity (laser Doppler), and superficial femoral artery blood flow (duplex ultrasound) were measured during immersion and for 30 minutes after immersion. Indices of vascular conductance were calculated (flux and blood flow/mean arterial pressure). Results: Reductions in rectal temperature (8°C, 0.2° ± 0.1°C; 22°C, 0.1° ± 0.1°C) and thigh skin temperature (8°C, 6.2° ± 0.5°C; 22°C, 3.2° ± 0.2°C) were greater in 8°C water than in 22°C (P < .01). Femoral artery conductance was reduced to a similar extent immediately after immersion (~30%) and 30 minutes after immersion (~40%) under both conditions (P < .01). In contrast, there was less thigh cutaneous vasoconstriction during and after immersion in 8°C water compared with 22°C (P = .01). Conclusion: These data suggest that immersion at both temperatures resulted in similar whole limb blood flow but, paradoxically, more blood was distributed to the skin in the colder water. This suggests that colder temperatures may be associated with reduced muscle blood flow, which could provide an explanation for the benefits of cold water immersion in alleviating exercise-induced muscle damage in sports and athletic contexts. Clinical Relevance: Colder water temperatures may be more effective in the treatment of exercise-induced muscle damage and injury rehabilitation because of greater reductions in muscle blood flow.