Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic structure of desert ground squirrels over a 20‐degree‐latitude transect from Oregon through the Baja California peninsula

The genetic structure of populations over a wide geographical area should reflect the demographic and evolutionary processes that have shaped a species across its range. We examined the population genetic structure of antelope ground squirrels (Ammospermophilus leucurus) across the complex of North American deserts from the Great Basin of Oregon to the cape region of the Baja California peninsula. We sampled 73 individuals from 13 major localities over this 2500‐km transect, from 43 to 22° north. Our molecular phylogeographical analysis of 555 bp of the mitochondrial cytochrome b gene and 510 bp of the control region revealed great genetic uniformity in a single clade that extends from Oregon to central Baja California. A second distinct clade occupies the southern half of the peninsula. The minimal geographical structure of the northern clade, its low haplotype diversity and the distribution of pairwise differences between haplotypes suggest a rapid northward expansion of the population that must have followed a northward desert habitat shift associated with the most recent Quaternary climate warming and glacial retreat. The higher haplotype diversity within the southern clade and distribution of pairwise differences between haplotypes suggest that the southern clade has a longer, more stable history associated with a southern peninsular refugium. This system, as observed, reflects both historical and contemporary ecological and evolutionary responses to physical environmental gradients within genetically homogeneous populations.
B Cell Receptor-Mediated Syk-Independent Activation of Phosphatidylinositol 3-Kinase, Ras, and Mitogen-Activated Protein Kinase Pathways 1

The Syk tyrosine kinase is a key molecule in the development of the B cell lineage and the activation of B lymphocytes after Ag recognition by the B cell Ag receptor (BCR). Several genetic studies with chicken B cells have reported that the recruitment of Syk by BCR is essential for activation of a cascade of signaling molecules including phosphatidylinositol 3-kinase, mitogen-activated protein kinases, Ras signaling pathways, phospholipase C-γ2 activation, and calcium mobilization. The identification of a Syk-deficient mouse IIA1.6/A20 B cell line provided us the opportunity to investigate Syk-mediated signaling in mouse. Surprisingly, phosphatidylinositol 3-kinase, Ras, and mitogen-activated protein kinases were activated upon BCR cross-linking in these Syk-deficient mouse B cells, whereas, as expected from results obtained in chicken B cells, phospholipase C-γ2 activation and calcium mobilization were impaired as well as the NF-κB pathway. These results indicate that BCR signaling is not strictly dependent on Syk expression in mouse IIA1.6/A20 B cells. Thus, B lymphocyte activation may be initiated by Syk-dependent and Syk-independent signaling cascades.
Serum antibody responses of juvenile and infant rhesus monkeys injected with Haemophilus influenzae type b and pneumococcus type 6A capsular polysaccharide-protein conjugates

Juvenile and infant rhesus monkeys were injected subcutaneously with saline solutions of Haemophilus influenzae type b (Hib) and pneumococcus type 6A (Pn6A) capsular polysaccharides conjugated to either tetanus toxoid (TT), horseshoe crab hemocyanin, or cholera toxin (CT), and the antibody responses of the monkeys to both bacterial components were measured. All three Hib conjugates were immunogenic and elicited booster responses; their comparative immunogenicity was Hib-CT greater than Hib-TT greater than Hib-horseshoe crab hemocyanin. Hib alone did not elicit antibodies in the juveniles. Juveniles responded earlier and with higher levels of antibodies than did infants. TT, as well as diphtheria-tetanus toxoids-pertussis vaccine adsorbed injected concurrently at a separate site, increased both Hib and TT antibody responses in juveniles (P less than 0.05). Concurrent injection of 5 Lf of fluid TT with a nonimmunogenic 5-micrograms dose in infants elicited levels of Hib antibodies comparable to those elicited by 50 micrograms of Hib-TT. Hib antibodies elicited by the conjugates remained at protective levels in both juveniles and infants 2 months after the last injection, were bactericidal, and conferred passive immunity against bacteremia in infant rats. Passive immunization of juveniles with tetanus immune globulin before each injection of Hib-TT did not suppress Hib antibodies. Hib-TT and Hib-CT elicited increases of Hib antibodies of the immunoglobulin M and G isotypes in the infants. The Pn6A-TT conjugate was considerably less immunogenic than the Hib-TT conjugate; only a few of the juveniles or infants responded with protective levels of Pn6A antibodies. Pn6A antibodies from responders conferred protection in mice against intraperitoneal challenge with Pn6A organisms. TT antibodies were elicited in both juvenile and infant animals after one injection of 50 micrograms of Hib-TT and in the infants injected with 5 micrograms of Hib-TT plus 5 Lf of TT; 5 micrograms of Hib-TT and Pn6A-TT in combination alone did not elicit TT antibodies. Hib-CT elicited CT antibodies in both juveniles and infants.
The Ecological Context of Life History Evolution

There is now a good theoretical understanding of life history evolution, and detailed explicit optimality models have been constructed. These present a challenge for empirical work examining some of the assumptions, such as the extent and mechanisms of the costs of growth and reproduction. In addition, there is an obvious need for comparative tests of the models. These tests, properly applied, may be particularly informative because they can deal with multiple independent variables, including ecological variables, and can reveal broad trends against a background of constraints on optima and the rate of evolutionary approach to them. Life histories are the probabilities of survival and the rates of reproduction at each age in the life-span. Reproduction is costly, so that fertility at all ages cannot simultaneously be maximized by natural selection. Allocation of reproductive effort has evolved in response to the demographic impact of different environments but is constrained by genetic variance and evolutionary history.
Transformed cells require continuous activity of RNA polymerase II to resist oncogene-induced apoptosis

Studies have indicated that deregulated oncogene expression can result in either programmed cell death or proliferation, depending on the cellular microenvironment. However, little is known about whether oncogenic signals in themselves are able to activate a cellular apoptotic program. We have tested the hypothesis that oncogenic signals in the absence of gene expression are sufficient to induce cell death, which would indicate that constitutive expression of antiapoptotic genes is necessary for maintenance of the transformed state. Using two highly specific RNA polymerase (RNAP) II inhibitors, 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) and alpha-amanitin, which inhibit RNAP II function by two distinct mechanisms, we found that inhibition of gene expression substantially increased apoptosis in a time- and dose-dependent manner in p53+/+- and p53(-/-)-transformed mouse embryonic fibroblasts and in HeLa cells, demonstrating that this type of apoptosis does not require wild-type p53. Engineered expression of an alpha-amanitin resistance RNAP II gene rendered cells resistant to induction of apoptosis by alpha-amanitin without affecting their sensitivity to DRB, indicating that alpha-amanitin induces apoptosis solely by inhibiting RNAP II function and not by a nonspecific mechanism. DRB-induced apoptosis was independent of the cell cycle or ongoing DNA replication, since DRB induced similar levels of apoptosis in asynchronous cells and cells synchronized by collection at mitosis. Inhibition of RNAP II in untransformed cells like Rat-1 or human AG1522 fibroblasts resulted not in apoptosis but in growth arrest. In contrast, deregulated expression of c-Myc in Rat-1 cells dramatically increased their sensitivity to DRB, directly demonstrating that apoptosis following inhibition of RNAP II function is greatly enhanced by oncogenic expression. The requirement for RNAP II function to prevent oncogene-induced apoptosis implies the need for the constitutive expression of an antiapoptotic gene(s) to maintain the transformed state. The differential sensitivities of untransformed and transformed cells to induction of apoptosis by transcriptional inhibition, coupled with the finding that this type of apoptosis is independent of p53 status, suggest that inhibition of RNAP II may be exploited therapeutically for the design of successful antitumor agents.
Why Vote for a Co-Opted Party? Endogenous Government Power Increases and Control of Opposition Politicians in Authoritarian Regimes

Why do voters in electoral autocracies vote for opposition parties that are co-opted by the government? The logic of electoral accountability should lead constituents to vote such parties out, and parties, knowing this, should never agree to be co-opted. Yet there is evidence that constituents often do not sanction opposition parties for failing to prevent the government from consolidating power. Standard accountability models suggest that this accountability failure is due to the parties having developed good reputations. This article develops a formal theory that offers a novel explanation for accountability failures specific to electoral autocracies. The theory shows how a consolidation of power by an authoritarian regime, increasing its ability to punish opposition politicians, can lead citizens not to vote opposition parties out of office even after seeing them fail to prevent a consolidation of power.
Iodine intake and thyroid carcinoma--a potential risk factor.

The role of enhanced thyroid-stimulating hormone (TSH) secretion, in the aetiology of thyroid cancer is not totally consistent. Circumstances and conditions which cause (e.g., iodine deficiency, through suboptimal intake in water and food) or indicate (e.g., goitre) increased TSH secretion have been associated to increased risk of thyroid cancer, most notably follicular and anaplastic carcinomas. Elevated incidence and mortality rates of thyroid cancer, however, are also found in areas were iodine intake is high (Hawaii, Iceland). At least in some countries (Switzerland), a favourable impact of the introduction of iodized salt on mortality from thyroid cancer has been reported. Elsewhere, the correction of iodine deficiency has coincided with elevations of diagnostic standards (e.g., spread of thyroid scintigraphy, ultrasound, and fine-needle biopsy) and corresponding increases in incidence of papillary carcinomas, often clinically silent, thus hampering a distinction of the two phenomena. Upward trends of papillary carcinoma incidence have, however, been seen in most affluent countries, irrespective of the iodine status of the population.
Effect of storage time on microtensile bond strength between quartz fiber post and composite core after different post surface treatments

Aim: The aim was to evaluate the influence of water storage on fiber post-resin composite adhesion after different postsurface treatments. Materials and Methods: Forty-two fiber posts were used. Half of them were treated by hydrogen-peroxide and the other half were sandblasted. The adhesive (Single Bond, 3M, USA) was applied on the post. Core was built-up using flowable composite (Ælite Flow, Bisco, USA). The specimens were divided into eight groups. Group 1 was treated with H2O2. Groups 2–4 were treated with H2O2 but stored for 3, 6, and 9 months, respectively. Groups 5–8 were sandblasted and stored for 0, 3, 6, and 9 months. μTBS was measured and data analyzed using one-way ANOVA and Tukey HSD. The fractured surfaces were evaluated by a stereomicroscope. The morphology of interfaces was assessed under SEM. H2O2-treated groups showed higher bond-strength. Results: The effect of “surface-treatment method” and “storage-time” was significant (P<0.0001), but there was no significant difference for their interaction effect (P=0.05). Water aging significantly decreased μTBS. Conclusions: Water aging significantly decreased microtensile bond strength regardless of the type of post surface treatment.
Detection of diarrheogenic Escherichia coli in children less than ten years old with and without diarrhea in New Caledonia using seven acetylaminofluorene-labeled DNA probes.

We report the use of seven acetylaminofluorene (AAF)-labeled DNA probes in evaluating the incidence of various Escherichia coli pathotypes in New Caledonia among 448 children with acute diarrhea (1,278 E. coli pathotypes studied) and 88 controls (264 E. coli pathotypes studied) in 1990. Diarrheogenic E. coli were detected using cloned gene probes for heat-labile and heat-stable enterotoxins, Shiga-like cytotoxins (SLTI and SLTII), the cell invasion phenotype (INV), and enteropathogenic-adherence factor (EAF). Isolates were also studied using bioassays and radioactive DNA probes as reference methods. Enterotoxigenic E. coli (ETEC) were isolated from only 5.36% of the patients; E. coli with localized adherence (LA) to HEp-2 cells was much more common in patients (14.4%) than in controls (3.4%; chi 2 = 7.54, P < 0.01), but most of the E. coli with an LA pattern were members of traditional enteropathogenic E. coli (EPEC) serogroups (chi 2 = 92.95, P < 0.001). Non-enteropathogenic E. coli with an LA pattern were weakly associated with diarrheal disease (8.9%). Escherichia coli with a diffuse or an aggregative pattern did not show a significant association with infantile diarrhea. Eight EPEC serogroups were identified and the frequency of positivity for the LA pattern was 70.5%; the EAF was significantly associated with the 0119:K9 serogroup. No enteroinvasive or SLT-producing E. coli were identified. An evaluation of the AAF probes in comparison with 32P-labeled probes and conventional bioassays was made during this epidemiologic survey. The positive and negative predictive values of the ETEC probes were 0.91 and 1, respectively (overall agreement = 99.8%). (ABSTRACT TRUNCATED AT 250 WORDS)
Effects of Vitrification on Outcomes of In VivoMature, In Vitro-Mature and Immature Human Oocytes

Background/Aims: To observe the effects of vitrification on spindle, zona pellucida, embryonic aneuploidy and DNA injury in in vivo-maruted, in vitro-mature and immature human oocytes. Methods: Between January 2009 and February 2015, 223 immature oocytes from 450 infertile patients, and 31 in vivo-mature oocytes from 3 infertile couples were collected. Of the 223 immature oocytes, 113 were used for in vitro culture before vitrification. Some oocytes were randomly divided into in vivo-mature group (group A, n = 15), in vitro-mature group (group B, n = 88) and immature group (group C, n = 85), and then the oocytes with spindle in these three groups after freezing-thawing were selected to use for Polscope imaging, embryonic aneuploidy screening and embryo development evaluation. Other oocytes were randomly divided into group A (n = 16), group B (n = 25) and group C (n = 25) for detecting DNA injury. Results: After thawing, spindle occurrence rate, spindle Retardance value, and cleavage rate were significantly higher in groups A and B than in group C (all P < 0.05), but there were no statistical differences in fertility rate, high-quality embryo rate, blastulation rate and aneuploidy rate amongst the three groups (all P > 0.05). Zona pellucida density (ZPD) was significantly lower in group A than in groups B and C both before and after vitrification (all P < 0.05). ZPD was significantly higher after thawing than before vitrification (all P < 0.05), but zona pellucida thickness (ZPT) was not significantly changed in all the three groups (all P > 0.05). Rate of comet cells was significantly lower in group A than in groups B and C (all P < 0.01). Comet tail was significantly longer in group C than in groups B and A (all P < 0.05). Conclusion: In vivo- and in vitro-mature human oocytes are more suitable to vitrification than immature human oocytes. Spindle Retardance value has more predictive value for embryonic development potential than ZPD and ZPT.
Update in the Epidemiology of Proximal Humeral Fractures

We sought to determine current trends in the number of fall-related and osteoporosis-related proximal humeral fractures in elderly Finns during last three decades. We collected data from the National Hospital Discharge Register on all patients 60 years or older who were admitted to Finnish hospitals from 1970 to 2002 for primary treatment of proximal humeral fractures. Fractures induced by traffic accidents or other high-energy traumas were excluded. The number and incidence (per 100,000 patients) of fractures increased from 208 (number) and 32 (incidence) in 1970 to 1120 (number) and 105 (incidence) in 2002. The age adjusted incidence of proximal humeral fractures also showed an increase, from 51 (1970) to 129 (2002) in women, and from 14 (1970) to 48 (2002) in men. In women 80 years or older, the age specific incidence of fracture increased from 90 (1970) to 294 (2002), while in the other age groups trend changes were less extensive. The mean patient age also increased, from 73 years (1970) to 78 years (2002) in women and from 70 years (1970) to 73 years (2002) in men. If these trends continue, the number of fractures in elderly Finns will triple during the next three decades.Level of Evidence: Prognostic study, Level IV (case series). See the Guidelines for Authors for a complete description of levels of evidence.
Intracellular alkalinization induced by bradykinin sustains activation of the constitutive nitric oxide synthase in endothelial cells.

The transient increase in [Ca2+]i in endothelial cells after stimulation with bradykinin can account for the initiation but not the sustained production of nitric oxide (NO). Therefore, we investigated whether this sustained activation of the constitutive NO synthase (cNOS) could be mediated by an increase in pHi, which is induced by an activation of the Na(+)-H+ exchanger rather than an increase in [Ca2+]i. Cultured human endothelial cells grown on coverslips were loaded with either C.SNAFL-2 or fura 2-AM for fluorometric analysis of either pHi or [Ca2+]i. NO release was assayed by the ability of effluent from endothelial cells to stimulate purified soluble guanylyl cyclase. The pH dependence of a microsomal cNOS preparation was determined by assay of L-[3H]citrulline formation from L-[3H]arginine. Bradykinin (10 nmol/L) induced a biphasic change in endothelial pHi consisting of an initial acidification followed by a prolonged alkalinization above resting values. Inhibition of the Na(+)-H+ exchanger using HOE 694 (10 mumol/L) prevented this increase in pHi. The L-citrulline assay revealed a twofold increase in cNOS activity on increasing pH from 6.7 to 7.4, an optimum at pH 7.5, and a complete abolition of activity at pH 8.6. Endothelial production of NO 15 minutes after starting the infusion of bradykinin was maintained at significantly higher levels in control cells compared with cells pretreated with HOE 694. The latter effect cannot be accounted for by an increase in intracellular Ca2+, since [Ca2+]i levels were not significantly different between the two groups. (ABSTRACT TRUNCATED AT 250 WORDS)
NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data

MOTIVATION In prognosis and survival studies, an important goal is to identify multi-biomarker panels with predictive power using molecular characteristics or clinical observations. Such analysis is often challenged by censored, small-sample-size, but high-dimensional genomic profiles or clinical data. Therefore, sophisticated models and algorithms are in pressing need. RESULTS In this study, we propose a novel Area Under Curve (AUC) optimization method for multi-biomarker panel identification named Nearest Centroid Classifier for AUC optimization (NCC-AUC). Our method is motived by the connection between AUC score for classification accuracy evaluation and Harrell's concordance index in survival analysis. This connection allows us to convert the survival time regression problem to a binary classification problem. Then an optimization model is formulated to directly maximize AUC and meanwhile minimize the number of selected features to construct a predictor in the nearest centroid classifier framework. NCC-AUC shows its great performance by validating both in genomic data of breast cancer and clinical data of stage IB Non-Small-Cell Lung Cancer (NSCLC). For the genomic data, NCC-AUC outperforms Support Vector Machine (SVM) and Support Vector Machine-based Recursive Feature Elimination (SVM-RFE) in classification accuracy. It tends to select a multi-biomarker panel with low average redundancy and enriched biological meanings. Also NCC-AUC is more significant in separation of low and high risk cohorts than widely used Cox model (Cox proportional-hazards regression model) and L1-Cox model (L1 penalized in Cox model). These performance gains of NCC-AUC are quite robust across 5 subtypes of breast cancer. Further in an independent clinical data, NCC-AUC outperforms SVM and SVM-RFE in predictive accuracy and is consistently better than Cox model and L1-Cox model in grouping patients into high and low risk categories. CONCLUSION In summary, NCC-AUC provides a rigorous optimization framework to systematically reveal multi-biomarker panel from genomic and clinical data. It can serve as a useful tool to identify prognostic biomarkers for survival analysis. AVAILABILITY AND IMPLEMENTATION NCC-AUC is available at http://doc.aporc. org/wiki/NCC-AUC. CONTACT ywang@amss.ac. cn SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Examination of passive ROM and capsular patterns in the hip.

BACKGROUND AND PURPOSE The present study was conducted to examine passive hip range of motion (PROM) for patients with hip dysfunction, including pain, with or without hip osteoarthritis, to arrange and describe PROM patterns and to count the number of hips presenting Cyriax's and Kaltenborn's capsular patterns. METHOD The study is theory-testing, observational, cross-sectional and descriptive. One hundred and sixty-eight patients (mean age 61.7 years, range 36-90 years), 50 with no hip osteoarthritis, 77 with unilateral hip osteoarthritis and 41 with bilateral osteoarthritis, based on radiological reports, were consecutively recruited by physicians in primary health care and orthopaedic settings. One examiner tested PROM bilaterally, by use of a goniometer and a standardized protocol. PROM limitations were calculated by comparing norms from the symptom-free hips (n = 100) in the study, from Kaltenborn and, in patients with unilateral hip osteoarthritis (n = 77), from the non-osteoarthritis hip. The limitations were arranged by size in PROM patterns. The patterns and the numbers of hips with patterns corresponding to Cyriax's and Kaltenborn's capsular patterns were counted. RESULTS Between 68 and 138 PROM patterns were identified by use of different PROM norms for defining limitations. Few osteoarthritis hips showed Cyriax's capsular pattern and none Kaltenborn's capsular pattern. CONCLUSIONS The concept of capsular pattern for the hip should be re-examined. No support was found in the present study for its existence. It is impossible to anticipate radiological evidence of hip osteoarthritis from the multitude of PROM patterns. Every patient should be regarded as unique.