Miracle-dz/UniFAR-FTUs huggingface dataset:
Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata.

PREMISE OF THE STUDY The ability of California tree populations to survive anthropogenic climate change will be shaped by the geographic structure of adaptive genetic variation. Our goal is to test whether climate-associated candidate genes show evidence of spatially divergent selection in natural populations of valley oak, Quercus lobata, as preliminary indication of local adaptation. METHODS Using DNA from 45 individuals from 13 localities across the species' range, we sequenced portions of 40 candidate genes related to budburst/flowering, growth, osmotic stress, and temperature stress. Using 195 single nucleotide polymorphisms (SNPs), we estimated genetic differentiation across populations and correlated allele frequencies with climate gradients using single-locus and multivariate models. RESULTS The top 5% of FST estimates ranged from 0.25 to 0.68, yielding loci potentially under spatially divergent selection. Environmental analyses of SNP frequencies with climate gradients revealed three significantly correlated SNPs within budburst/flowering genes and two SNPs within temperature stress genes with mean annual precipitation, after controlling for multiple testing. A redundancy model showed a significant association between SNPs and climate variables and revealed a similar set of SNPs with high loadings on the first axis. In the RDA, climate accounted for 67% of the explained variation, when holding climate constant, in contrast to a putatively neutral SSR data set where climate accounted for only 33%. CONCLUSIONS Population differentiation and geographic gradients of allele frequencies in climate-associated functional genes in Q. lobata provide initial evidence of adaptive genetic variation and background for predicting population response to climate change.
The effects of active videogames on BMI among young people: A meta-analysis

The objective of this chapter is a systematic review and meta-analysis was performed to quantify the effectiveness of active videogames (AVGs) as obesity prevention interventions aimed at children and adolescents. The method is studies were included that focused on children or adolescents (=18 years), assessed BMI as the outcome measure, used one or more AVGs as intervention, employed a controlled experimental design, used BMI as an outcome measure, enrolled participants up to and including 18 years of age, and comprised original studies. Employing these inclusion criteria, nine studies were included in the meta-analysis. The results are active videogames had a small to medium-sized and significant average effect on children and adolescents: Hedges' g = 0.38 (95% CI: 0.00 - 0.77). Heterogeneity was substantial (I2 = .91) but neither participants' weight status, nor sample size, intervention duration or dropout moderated the effect of AVGs. The conclusion of this chapter is the results of this meta-analysis provide preliminary evidence that active videogames can decrease BMI among children/adolescents.
Selective degeneration of optic nerve fibres in the cat produced by a pressure block.

Using a technique described previously, we have applied pressure to the optic nerve of a cat sufficient to cause conduction block of the t1 response (the response of the Y optic nerve fibres). A greater pressure, usually sufficient to cause a transient block of the t2 response (the response of the X fibres), leads to degeneration of the Y axons caudal to the block. This is demonstrated by the disappearance of the t1 response in this region after 4‐5 days and by the presence in electron micrographs of degenerating large (Y) fibres. Some small fibres also show degeneration, but the medium (X) fibres are largely spared. The time course of loss of response in the Y fibres is similar whether the loss is due to a pressure block or to enucleation, suggesting that the pressure block as used by us causes a disruption of the axon. If the pressure is great enough to block part of the t2 response (X fibres) there is also a similarity in time course of loss of response to that following enucleation. Both for the enucleated and the pressure‐blocked cat the t2 response fails about 1 day before the t1 response. This is in apparent disagreement with the morphological findings in the literature, confirmed here, indicating an earlier degeneration of the larger fibres. The post‐synaptic response in the lateral geniculate nucleus to the t1 input (the r1 response) also fails about 1 day before the t1 response. In the visual cortex the loss of the r1 response reveals more clearly than is normally possible an r2 response, the response of the X optic radiation fibres. The response in the optic nerve or tract to a bright flash of light is dominated by the response of the Y fibres. When these are blocked the response is greatly reduced.
Targeting Radiation-Induced G2 Checkpoint Activation with the Wee-1 Inhibitor MK-1775 in Glioblastoma Cell Lines

The purpose of this study was to determine the capacity of MK-1775, a potent Wee-1 inhibitor, to abrogate the radiation-induced G2 checkpoint arrest and modulate radiosensitivity in glioblastoma cell models and normal human astrocytes. The radiation-induced checkpoint response of established glioblastoma cell lines, glioblastoma neural stem (GNS) cells, and astrocytes were determined in vitro by flow cytometry and in vivo by mitosis-specific staining using immunohistochemistry. Mechanisms underlying MK-1775 radiosensitization were determined by mitotic catastrophe and γH2AX expression. Radiosensitivity was determined in vitro by the clonogenic assay and in vivo by tumor growth delay. MK-1775 abrogated the radiation-induced G2 checkpoint and enhanced radiosensitivity in established glioblastoma cell lines in vitro and in vivo, without modulating radiation response in normal human astrocytes. MK-1775 appeared to attenuate the early-phase of the G2 checkpoint arrest in GNS cell lines, although the arrest was not sustained and did not lead to increased radiosensitivity. These results show that MK-1775 can selectively enhance radiosensitivity in established glioblastoma cell lines. Further work is required to determine the role Wee-1 plays in checkpoint activation of GNS cells. Mol Cancer Ther; 10(12); 2405–14. ©2011 AACR.
Electrically Evoked Compound Action Potentials Recorded from Subjects who Use the Nucleus CI24M Device

The ability to directly measure the response to a pulse with the NRT opens the possibility of using this system to characterize the responses to more complex stimuli. An example is the responses to constant-amplitude pulse trains. With further changes in the software that controls the implant, it may be possible to characterize the responses to modulated pulse trains or other stimuli that better approximate the type of stimuli that are normally used with a cochlear implant speech processor.
Proximate nutritional composition and antioxidant properties of Oryza rufipogon, a wild rice collected from Malaysia compared to cultivated rice, MR219.

Wild rice (Oryza rufipogon L) is known as an important germplasm that has specific desirable attributes and a high genetic diversity. The physicochemical and antioxidant properties of O. rufipogon Griff. (acc. IRGC105491), a wild rice collected from Malaysia that was used in a breeding program and a QTL mapping study, were assessed to determine the rice’s nutritional value compared with a commonly consumed rice cultivar MR219 (O. sativa subsp. indica). To identify and quantify the phenolic compounds in the rice extracts, Ultra Performance Liquid Chromatography (UPLC) coupled with a photodiode array detector (PDA) was applied. The results obtained were supported by a determination of the total phenolic compounds (TPC), 2,2-diphenyl-1-picrylhydrazyl (DPPH • ) radical scavenging, tocopherols, tocotrienols, and the ferric reducing ability power (FRAP) of the respective extracts originating from the whole grain. The results indicated that O. rufipogon, irrespective of its poor appearance, contained high proximate nutritional composition and antioxidant properties. The grain of O. rufipogon consisted of 8.0% protein, 2.2% fat, and 25.0% amylose content
Glycosylation of Homologous Immunodominant Proteins of Ehrlichia chaffeensis and Ehrlichia canis

ABSTRACT The glycoprotein genes of Ehrlichia chaffeensis (1,644 bp) and Ehrlichia canis (2,064 bp) encode proteins of 548 to 688 amino acids with predicted molecular masses of only 61 and 73 kDa but with electrophoretic mobilities of 120 kDa (P120) and 140 kDa (P140), respectively. The 120-kDa protein gene of E. chaffeensis contains four identical 240-bp tandem repeat units, and the 140-kDa protein gene of E. canis has 14 nearly identical, tandemly arranged 108-bp repeat units. Conserved serine-rich motifs identified in the repeat units of P120 and P140 were also found in the repeat units of the human granulocytotropic ehrlichiosis agent 130-kDa protein and of the fimbria-associated adhesin protein Fap1 ofStreptococcus parasanguis. Nearly the entire (99%)E. chaffeensis P120 gene (1,616 bp), the 14-repeat region (78%) of the E. canis P140 gene (1,620 bp), and a 2-repeat region from the E. chaffeensis P120 gene (520 bp) were expressed in Escherichia coli. The recombinant proteins exhibited molecular masses ranging from 1.6 to 2 times larger than those predicted by the amino acid sequences. Antibodies against the recombinant proteins reacted with E. chaffeensis P120 andE. canis P140, respectively. Carbohydrate was detected on the E. chaffeensis and E. canis recombinant proteins, including the two-repeat polypeptide region of E. chaffeensis P120. A carbohydrate compositional analysis identified glucose, galactose, and xylose on the recombinant proteins. The presence of only one site for N-linked (Asn-Xaa-Ser/Thr) glycosylation, a lack of effect of N-glycosidase F, the presence of 70 and 126 Ser/Thr glycosylation sites in the repeat regions of P120 and P140, respectively, and a high molar ratio of carbohydrate to protein suggest that the glycans may be O linked.
Improving Generalization Performance by Switching from Adam to SGD

Despite superior training outcomes, adaptive optimization methods such as Adam, Adagrad or RMSprop have been found to generalize poorly compared to Stochastic gradient descent (SGD). These methods tend to perform well in the initial portion of training but are outperformed by SGD at later stages of training. We investigate a hybrid strategy that begins training with an adaptive method and switches to SGD when appropriate. Concretely, we propose SWATS, a simple strategy which switches from Adam to SGD when a triggering condition is satisfied. The condition we propose relates to the projection of Adam steps on the gradient subspace. By design, the monitoring process for this condition adds very little overhead and does not increase the number of hyperparameters in the optimizer. We report experiments on several standard benchmarks such as: ResNet, SENet, DenseNet and PyramidNet for the CIFAR-10 and CIFAR-100 data sets, ResNet on the tiny-ImageNet data set and language modeling with recurrent networks on the PTB and WT2 data sets. The results show that our strategy is capable of closing the generalization gap between SGD and Adam on a majority of the tasks.
The Golem: What Everyone Should Know about Science

The Mathematical Association of America, 1993 372 pages $35.00 "A Cat That Can't Be Caught" is the first chapter of this quite readable story of the life of Eric Temple Bell. Constance Reid carries us along on her private-eye-like search for the truth about his early years, which he had kept secret from his friends, his family, and even from his beloved wife, and which he had even distorted (the polite word) when filling out a form for the Cal tech administration in 1943. By a combination of diligence and luck the author has discovered that when Bell was about a year old his father moved the family from Scotland to San Jose, thence south to the farm country of Santa Clara County, where he began a fruit orchard. It was here that Bell spent his boyhood, and images of an idealized pastoral countryside find their way into many of his poems and stories. Why was it necessary for him to keep these years secret? Reid never finds this out. He was a teenager when his father died, and his mother rerurned the family to England, where Bell entered what we would call a high school and fell in love with mathematics. But it was back in the United States that Bell did his university work-Stanford, Washington, and Columbia. After finishing his PhD, he began his teaching career and for many years seemed to want little more. Mathematical research was a minor activity. Poetry demanded more attention, and it was the time for beginning an epic work, The Scarlet Night, the revision of which was to occupy the last years of his life. It was also the time for his marriage, at the age of 27, to his beloved Toby. The author said to Bell's son Taine: "The thought has passed my mind that your father might have preferred being a poet to being a mathematician," to which Taine replied, "I think he might have ifhe had had any success. " Bell found no conflict between his dual interests, and wrote that "mathematics and poetry are simply isomorphic. " His mathematical research began to expand in original directions, which were, however, apparently not very well described in his publications. One of the reviewers contacted by Reid had two favorite instances of Bell's style: "the following complete sentence: 'Hence, etc.' and my very favorite footnote: 'A set of elements form a semi-group if they have the group property, etc. ", A few years later his "recreational writing" began under the name of John Taine (the basis for the name is obscure-it is not in his family history) in the genre we now call science fiction. A friend suggested that it served "as a relief from the grind of mathematics. " Although Reid comments clearly on Bell's fictional products, her descriptions of his mathematics is another matter; for
The effects of supplementary bacterial phytase on dietary true metabolisable energy, nutrient digestibility and endogenous losses in precision fed turkeys

1. A total of 40 female BUT9 turkeys were used in a precision-feeding assay to investigate the effect of dietary phytase on true metabolisable energy corrected for N retention (TME N ), coefficients of true dry matter (TDMD), mineral, amino acid and nitrogen (TND) digestibilities and the excretion of endogenous mucin, measured as sialic acid (SA). 2. Five treatments were used in this study: control (C), C + 250 phytase units (FTU) per kg feed, C + 500 FTU, C + 2500 FTU, and glucose only for endogenous losses estimation. Diets were formulated to be nutritionally adequate with the exception that the P content was relatively low (3·6 g/kg non-phytate P). 3. Inclusion of phytase increased TND in a quadratic manner with the optimum being achieved at approximately 500 FTU, at which TND was 37 % greater than in the control. The concentration of SA in the excreta decreased linearly with increased phytase supplementation. Dietary TME N , TDMD and true mineral digestibility coefficients were not significantly affected by phytase supplementation. 4. Phytase inclusion increased digestibility coefficients for indispensable, dispensable and total amino acids in a linear manner. The scale of the response to phytase was greatest with threonine and least with lysine digestibility, suggesting a specific mechanism of action that benefits gut health. 5. The strong negative relationship between secretion of SA and threonine digestibility suggests that a large part of the threonine benefit may be from reduced mucin synthesis. This supports the hypothesis that dietary phytase may play a role in improving the health status of the intestine and, as a result, reduces the maintenance energy requirements of turkeys.
Efficacy of chlorhexidine and green tea mouthwashes in the management of dental plaque-induced gingivitis: A comparative clinical study

Background: The intake of green tea has been increased recently due to its medicinal values. The antibacterial and antioxidant properties of green tea were found to be beneficial in the treatment of gingival and periodontal diseases. The aim of this comparative study was to compare the efficacy of the mouthwash containing green tea and chlorhexidine in the management of dental plaque-induced gingivitis. Materials and Methods: Thirty patients who participated in the study were divided randomly into two groups, each group of 15 patients was prescribed with either chlorhexidine or green tea mouthwash. Turesky modification of Quigley-Hein plaque index, Löe and Silness gingival index, Ainamo and Bay bleeding index, tooth stain, and tongue stain (TS) were recorded at baseline, 15 days, and 1 month. The subjects were asked to report any discomfort or alteration in taste. Results: There was a significant decrease in plaque index, gingival index, and bleeding index in both the groups. However, green tea mouthwash resulted in a statistically significant decrease in bleeding index compared to chlorhexidine group. There was no significant difference in tooth stain and TS in both the groups. Conclusion: The green tea-containing mouthwash is equally effective in reducing the gingival inflammation and plaque to chlorhexidine.
Pathogenicity of atypical Aeromonas salmonicida in Atlantic salmon compared with protease production

The pathogenicity of extracellular products (ECPs) from 24 atypical Aeromonas salmonicida strains was studied with respect to : lethality in Atlantic salmon, pathogenic effect in muscle, haemolytic activity, cytotoxicity in two fish cell lines and proteolytic activities. Furthermore, the relationship between lethality of ECPs and mortality caused by bacterial challenge was examined. Correlation was demonstrated between the pathogenic properties and proteolytic activities of the ECPs. Cytolytic (GCAT) activity comparable with that of the typical reference strain used (NCMB 1102) was not detected in ECPs of any of the atypical strain tested. An extracellular metallo‐caseinase, AsaP1, was linked with lethal toxicity and a strong pathogenic effect. Furuncular‐like lesions were produced by ECPs containing AsaP1 activity. One strain produced a lethal toxin which was neither caseinolytic nor with GCAT comparable activity. The examined atypical strains form at least three distinct groups based on different virulence mechanisms and extracellular proteases.
Familial thyroxine-binding globulin deficiency. A study of three Danish families.

Three Danish pedigrees have been studied with a view to reduced thyroxine-binding globulin (TBG). The study confirmed that this defect is transmitted by X-chromosome-linked dominant inheritance, there being no man-to-man transmission, but also that it may occur in two types: deficient TBG and low, non-zero TBG. Definite changes of TBG and thyroid function tests were found in the hemizygous men, whereas the heterozygous women showed a marked variation in the range between the values for hemizygous men and normal persons. Determination of total thyroxine appears to afford more guidance than the protein-bound iodine suggested by others. Two of four women on oral contraception exhibited such deviating TBG values that they are assumed to be TBG heterozygous. In all persons free thyroxine proved normal or slightly reduced but all the persons tested were euthyroid. However, the propositus of one family had previously been treated for Graves' disease.
Psychophysiologic Response Patterns in Migraine Before and After Temperature Biofeedback: Prediction of Treatment Outcome

Psychophysiologic response patterns were studied in female migraine patients during headache-free periods (n = 16) and in controls (n = 8). Cardiovascular variables studied were heart rate (HR) and temporal artery pulse wave amplitudes (PWA). Phasic responses to 80-dB, 1000-Hz tones, each lasting 2 sec and sounded at irregular intervals, were studied within a habituation laboratory design. In addition, electromyographic (EMG) levels from the frontal muscles and hand temperature were measured. HR responses were less pronounced and PWA reduction more pronounced in migraine patients than in controls. There were no differences between migraine patients and controls in habituation pattern. Migraine patients showed lower hand temperature and higher EMG levels than controls. Migraine patients were treated with eight temperature biofeedback sessions and were evaluated clinically and psychophysiologically during and 2 months after treatment. Clinical follow-up evaluation was done 2 years after treatment. An average reduction in headache frequency of 66% was reported. A relationship between HR and PWA response pattern before treatment and treatment outcome was found. Migraine patients reporting most pronounced clinical improvement showed a “normalization” of the PWA response pattern after treatment.
Methods for improving the efficiency of estimating total osteon density in the human anterior mid-diaphyseal femur.

In order to preserve whole bone integrity and minimize destruction, paleohistologists often rely on histomorphometric data obtained from small areas (1.5-50 mm2) sampled within the anterior mid-diaphyseal femur. Because bone exhibits significant histological variation, the validity of results based on such sampling is questionable. The accuracy of various subareas (columns, rows, squares approximating dimensions and locations assessed by paleohistologists) in predicting total osteon density in the anterior mid-diaphyseal femur is assessed in the present study. Thirty-five specimens (12.7 mm wide, 100 microm thick, average area 56.7 mm2) were chosen at random from a skeletal population of 94 Inuits and Pueblo agriculturists. The specimens were photographed and enlarged; an acetate grid (12 columns, 10 rows, 120 squares, square = 1 mm2 of bone surface) was superimposed over the photograph; and secondary osteons and fragments were identified. Alternate columns (50% total area, T.Ar) predicted over 98% of entire section total osteon density. Two column combinations (15% T.Ar), separated by at least one column, predicted 91 to 95% of total osteon density. Individual column (8% T.Ar) predictability ranged from 48 to 86%. Two row combination (32 to 40% T.Ar) predictability values ranged from 86 to 95%. Individual rows (<1 to 20% T.Ar) predicted from 45 to 92% of total variation. Combinations of squares approximating areas and locations assessed by other paleohistologists ranged in predictability values from 80 to 94%. The results demonstrate that subareas of as little as 15% predict 95% of variation in total osteon density in the entire anterior mid-diaphyseal femoral section. A minimization of histological area evaluated without the loss of accuracy allows for a minimization of time invested in data collection and the utilization of partially damaged specimens.