Miracle-dz/UniFAR-FTUs huggingface dataset:
Interleukin-4 and -8 gene polymorphisms and risk of gastric cancer in a population in Southwestern China.

BACKGROUND Gastric carcinogenesis is a complicated process that involves environmental and genetic factors like interleukin-4 (IL-4) and IL-8. Single nucleotide polymorphisms in their genes are associated with changed levels of gene expression. Here, we investigated the association between IL4-590 C>T and IL8-251T>A and gastric cancer (GC) risk in Sichuan of Southwestern China. MATERIALS AND METHODS We surveyed the research subjects using a self-designed questionnaire with questions on demographic factors and putative risk factors. Approximately 2-5ml of whole blood was collected after field survey to analyze IL4-590 C>T and IL8-251T>A genotypes using MALDI-TOF MS. RESULTS Our study recruited 308 pairs of GC patients and controls, including 224 (72.7%) men and 84 (27.3%) women in each group. There were 99 cardia and 176 noncardia GC patients in the case group. The case and control groups had an average age of 57.7±10.6 (mean±SD) and 57.6±11.1 years. GC patients reported a significantly greater proportion of family history of cancer (29.9% vs 10.7%, p<0.01) and drinking (54.6% vs 43.2%, p<0.01) than did controls. Variant genotypes of IL-4-590 C>T and IL-8-251 T>A were not associated with overall GC risk (adjusted OR, 0.89; 95%CI, 0.61-1.28 for CT or CC vs TT; adjusted OR, 1.14; 95%CI, 0.86-1.79 for TA or AA vs TT). Stratification analysis of two SNPs for risk by subsites only found that variant IL-8-251 TA or AA genotype was associated with increased noncardia GC risk (adjusted OR, 2.58; 95%CI, 1.19-5.57). We did not observe interactions between the IL-8-251 T>A genotype and smoking (adjusted OR, 0.38; 95%CI, 0.08-1.79) or drinking (adjusted OR, 0.36; 95%CI, 0.08-1.65) for risk of noncardia GC. CONCLUSIONS Our data indicate no association between the two SNPs of IL-4-590 and IL-8-251 with overall GC risk, while the IL-8-251 TA or AA genotype conferred risk of cardia GC. Our findings contribute to the evidence body for risk of SNPs associated with the development of gastric cancer in this region.
Not Noble Savages After All: Limits to Early Altruism

Many scholars draw on evidence from evolutionary biology, behavioral economics, and infant research to argue that humans are “noble savages,” endowed with indiscriminate kindness. We believe this is mistaken. While there is evidence for an early-emerging moral sense—even infants recognize and favor instances of fairness and kindness among third parties—altruistic behaviors are selective from the start. Babies and young children favor people who have been kind to them in the past and favor familiar individuals over strangers. They hold strong biases for in-group over out-group members and for themselves over others, and indeed are more unequivocally selfish than older children and adults. Much of what is most impressive about adult morality arises not through inborn capacities but through a fraught developmental process that involves exposure to culture and the exercise of rationality.
Power of the Spacing test for Least-Angle Regression

Recent advances in Post-Selection Inference have shown that conditional testing is relevant and tractable in high-dimensions. In the Gaussian linear model, further works have derived unconditional test statistics such as the Kac-Rice Pivot for general penalized problems. In order to test the global null, a prominent offspring of this breakthrough is the spacing test that accounts the relative separation between the first two knots of the celebrated least-angle regression (LARS) algorithm. However, no results have been shown regarding the distribution of these test statistics under the alternative. For the first time, this paper addresses this important issue for the spacing test and shows that it is unconditionally unbiased. Furthermore, we provide the first extension of the spacing test to the frame of unknown noise variance. More precisely, we investigate the power of the spacing test for LARS and prove that it is unbiased: its power is always greater or equal to the significance level $\alpha$. In particular, we describe the power of this test under various scenarii: we prove that its rejection region is optimal when the predictors are orthogonal; as the level $\alpha$ goes to zero, we show that the probability of getting a true positive is much greater than $\alpha$; and we give a detailed description of its power in the case of two predictors. Moreover, we numerically investigate a comparison between the spacing test for LARS and the Pearson's chi-squared test (goodness of fit).
Assessing the marks of change: how psychotherapy alters the brain structure in women with borderline personality disorder.

BACKGROUND There is increasing evidence that psychotherapy can alter the function of the brain of patients with borderline personality disorder (BPD). However, it is not known whether psychotherapy can also modify the brain structure of patients with BPD. METHODS We used structural MRI data of female patients with BPD before and after participation in 12 weeks of residential dialectical behavioural therapy (DBT) and compared them to data from female patients with BPD who received treatment as usual (TAU). We applied voxel-based morphometry to study voxel-wise changes in grey matter volume over time. RESULTS We included 31 patients in the DBT group and 17 in the TAU group. Patients receiving DBT showed an increase of grey matter volume in the anterior cingulate cortex, inferior frontal gyrus and superior temporal gyrus together with an alteration of grey matter volume in the angular gyrus and supramarginal gyrus compared with patients receiving TAU. Furthermore, therapy response correlated with increase of grey matter volume in the angular gyrus. LIMITATIONS Only women were investigated, and groups differed in size, medication (controlled for) and intensity of the treatment condition. CONCLUSION We found that DBT increased grey matter volume of brain regions that are critically implicated in emotion regulation and higher-order functions, such as mentalizing. The role of the angular gyrus for treatment response may reside in its cross-modal integrative function. These findings enhance our understanding of psychotherapy mechanisms of change and may foster the development of neurobiologically informed therapeutic interventions.
Integrating Reactive Behavior and Planning: Optimizing Execution Time Through Predictive Preparation of State Machine Tasks

Tasks that change the physical state of a robot take a considerable amount of time to execute. However, many robot applications spend the execution time waiting, although the following tasks might require time to prepare. This paper proposes to amend tasks with a description of their expected outcomes, which allows planning successive tasks based on this information. The suggested approach allows sequential and parallel composition of tasks, as well as reactive behavior modeled as state machines. The paper describes the means of modeling and executing these tasks, details different possibilities of planning in state machine tasks, and evaluates the benefits achievable using the approach.
Increased cytokines in cystic fibrosis patients’ upper airways during a new P. aeruginosa colonization

Previously, we found linkages of inflammatory mediator levels in CF upper airways (UAW) sampled by nasal lavage (NL) to disease severity and to chronic pathogen colonization such as Pseudomonas aeruginosa (PsA). Here, we assess UAW cytokine dynamics in CF patients with a new PsA colonization.
Increased levels of platelet activation markers are positively associated with carotid wall thickness and other atherosclerotic risk factors in obese patients

Summary The role of platelets in the development of atherosclerosis and obesity-related prothrombotic state is still under investigation. In this cross-sectional cohort study, we measured the levels of different platelet activation markers and evaluated their relationship with carotid intima-media thickness (IMT) along with other atherosclerotic risk factors in obese patients with or without atherosclerotic co-morbidities. We enrolled 154 obese patients, including 98 with either hypertension, type 2 diabetes mellitus or dyslipidaemia, 56 without these co-morbidities and 62 age- and sex-matched healthy controls. Platelet P-selectin expression and the number of platelet-derived microparticles (PMPs) were measured by flow cytometry; soluble P-selectin levels were analysed by ELISA and Thr715Pro P-selectin polymorphism was determined by PCR-RFLP. Carotid IMT was examined by ultrasonography. The levels of platelet activation parameters were significantly elevated in all obese subjects with increased carotid IMT compared to healthy controls. There was no effect of Thr715Pro genotype on soluble P-selectin levels in obese individuals contrary to normal subjects. Significant and positive association was revealed between carotid IMT and platelet P-selectin (p<0.0001), soluble P-selectin (p=0.039) and PMP (p=0.0001) levels. After adjusting for multiple variables, independent association was found between soluble P-selectin and fibrinogen (p=0.007), PMP levels and body mass index (p<0.0001) as well as platelet P-selectin and carotid IMT (p=0.012) plus plasminogen activator inhibitor-1 (p=0.009). In conclusion, P-selectin and PMP levels showed positive associations with abnormal carotid IMT and other risk factors in obesity suggesting a critical role of enhanced platelet reactivity in atherosclerotic wall alteration.
Robust Identification of Periodic Systems with Applications to Texture Inpainting.

In this paper we address the problem of robust identification of discrete LTI systems that have a periodic impulse response. The main result of the paper shows that this problem can be solved by factoring a suitable defined Hankel operator. These results are illustrated with a practical example arising in the context of image processing: completing a textured image where some pixels are missing.
Fly Genes That Help Devour a Fungal Parasite

BackgroundUterine fibroids or leiomyoma are a common benign smooth muscle tumor. The tumor growth is well known to be estrogen-dependent. However, the molecular mechanisms of its estrogen-dependency is not well understood.MethodsDifferentially expressed genes in human uterine fibroids were either retrieved from published papers or from our own statistical analysis of downloaded array data. Probes for the same genes on different Affymetrix chips were mapped based on probe comparison information provided by Affymetrix. Genes identified by two or three array studies were submitted for ortholog analysis. Human and rat ortholog genes were identified by using ortholog gene databases, HomoloGene and TOGA and were confirmed by synteny analysis with MultiContigView tool in the Ensembl genome browser.ResultsBy integrated analysis of three recently published DNA microarray studies with human tissue, thirty-eight genes were found to be differentially expressed in the same direction in fibroid compared to adjacent uterine myometrium by at least two research groups. Among these genes, twelve with rat orthologs were identified as estrogen-regulated from our array study investigating uterine expression in ovariectomized rats treated with estrogen. Functional and pathway analyses of the twelve genes suggested multiple molecular mechanisms for estrogen-dependent cell survival and tumor growth. Firstly, estrogen increased expression of the anti-apoptotic PCP4 gene and suppressed the expression of growth inhibitory receptors PTGER3 and TGFBR2. Secondly, estrogen may antagonize PPARγ signaling, thought to inhibit fibroid growth and survival, at two points in the PPAR pathway: 1) through increased ANXA1 gene expression which can inhibit phospholipase A2 activity and in turn decrease arachidonic acid synthesis, and 2) by decreasing L-PGDS expression which would reduce synthesis of PGJ2, an endogenous ligand for PPARγ. Lastly, estrogen affects retinoic acid (RA) synthesis and mobilization by regulating expression of CRABP2 and ALDH1A1. RA has been shown to play a significant role in the development of uterine fibroids in an animal model.ConclusionIntegrated analysis of multiple array datasets revealed twelve human and rat ortholog genes that were differentially expressed in human uterine fibroids and transcriptionally responsive to estrogen in the rat uterus. Functional and pathway analysis of these genes suggest multiple potential molecular mechanisms for the poorly understood estrogen-dependent growth of uterine fibroids. Fully understanding the exact molecular interactions among these gene products requires further study to validate their roles in uterine fibroids. This work provides new avenues of study which could influence the future direction of therapeutic intervention for the disease.
Limit Laws for Heights in Generalized Tries and PATRICIA Tries

Wojciech Szpankowskit Department of Computer Science Purdue University W. LafayeUe, IN 47907 UB.A. spa@cs.purdue. edu We consider digital trees such as (generalized) tries and PATRICIA tries, built from n random strings generated by an unbiased memoryless source (i.e., all symbols are equally likely). We study limit laws of the height which is defined as the longest path in such trees. It turns out that this height also represents the number of random questions required to recognize n distinct objects. We shall identiry three natural regions of the height distribution~. For tries, in the region where most of the probability mas~ is concentrated, the asymptotic distribution is of extreme value type (Le., double exponential distribution). Surprisinglyenough, the height of the PATIUCIA trie behaves quite differently in this region; It exhibits an exponential of a Gaussian distribution (with an oscillating tcnn) around the most probable value k l = llog2 n + /21og2 n ~ ~J+l. In fact, the asymptotic distribution of PATIUCIA height concentrates on one or two points. For most n all the ma. "iS is concentrated at kI , however, there exist subsequences of n such that the mass is on the two points hI 1 and hI, or kI and hi + 1. We derive these results by a combination of analytic methods such as generating functions, Mellin transform, the saddle point method and ideas of applied mathematics such as linearization, asymptotic matching and the WKB method. We present also some numerical verification of our results.
Laccaic Acid A Is a Direct, DNA-competitive Inhibitor of DNA Methyltransferase 1*

Background: Approved DNA demethylators do not directly inhibit Dnmt1, an oncogenic methyltransferase. Results: Laccaic acid A (LCA) is a direct, DNA-competitive Dnmt1 inhibitor that reactivates genes silenced by DNA methylation in breast cancer cells synergistically with 5-azadC. Conclusion: LCA is a natural product in a new class of Dnmt1-targeting small molecules. Significance: By directly inhibiting Dnmt1, we may reveal and block specific carcinogenesis pathways. Methylation of cytosines in CpG dinucleotides is the predominant epigenetic mark on vertebrate DNA. DNA methylation is associated with transcriptional repression. The pattern of DNA methylation changes during development and with disease. Human DNA methyltransferase 1 (Dnmt1), a 1616-amino acid multidomain enzyme, is essential for maintenance of DNA methylation in proliferating cells and is considered an important cancer drug target. Using a fluorogenic, endonuclease-coupled DNA methylation assay with an activated form of Dnmt1 engineered to lack the replication foci targeting sequence domain, we discovered that laccaic acid A (LCA), a highly substituted anthraquinone natural product, is a direct inhibitor with a 310 nm Ki. LCA is competitive with the DNA substrate in in vitro methylation assays and alters the expression of methylated genes in MCF-7 breast cancer cells synergistically with 5-aza-2′-deoxycytidine. LCA represents a novel class of Dnmt-targeted molecular probes, with biochemical properties that allow it to distinguish between non DNA-bound and DNA-bound Dnmt1.
Magnetization dynamics in racetrack memory

Magnetization Dynamics in Racetrack Memory Various devices have been proposed which use magnetic domain walls (DWs) in nanosized magnetic structures to perform logic operations or store information. In particular in ‘Racetrack memory’ bits of information represented by DWs are shifted in a magnetic wire to be stored. For these memory and logic devices to be successful, great control of DW motion is of vital importance. In cooperation with IBM’s Almaden research laboratory a pump-probe Kerr magnetooptical scanning microscope has been developed. In order to control DW injection, motion and reset, magnetic fields have to be applied locally on the nanowire. For this a special Damascene CMOS chip has been fabricated at the 200 mm wafer facility at IBM Microelectronics Research Laboratory (MRL). Probing of the local magnetization is done with a focused pulsed laser spot of 400 nm diameter where the polarization rotation caused by the Kerr effect is measured after reflection. In order to achieve optimal focusing a perpendicular incident laser beam is focused with a high numerical aperture objective. Synchronized ‘pumping’ in this scheme is achieved by successively: 1 injecting a DW; 2 propagate the DW down the nanowire with either current through or an applied field pulse over the nanowire; 3 and finally resetting the whole nanowire to its original magnetization by applying a large field together with the injection of an opposite magnetic domain. With this setup field and current induced DW motion is studied in permalloy nanowires ranging in width from 200 to 700 nm and thickness of 20 nm. For control of DWs in Racetrack memory it is important to understand the different mechanism for driving a DW already in motion (dynamic) and driving a DW that is currently at rest (static). The propagation field, the minimum field below which no DW motion takes place, is measured for both dynamic DWs and static DWs. It is found that Static DWs require a much higher field than DWs already in motion. A model is build where this effect is related to the wire roughness, successfully describing the existence of a propagation field, the difference between both propagation fields and a specific effect related to the method of injection.
Geographic variation in the foraging behaviour, diet and chick growth of rockhopper penguins

The foraging ecology of rockhopper penguins was investigated at 3 sites marked by contrasting ecological conditions. The northern subspecies was studied at Amsterdam Island (AMS) in oceanic subtropical waters, and the southern subspecies at the Kerguelen Archipelago (KER) in a subantarctic coastal habitat and at the Crozet Archipelago (CRO) in subantarctic neritic waters. During the brooding period, females from every site mainly made daily foraging trips lasting 11 to 12 h. A principal component analysis (PCA) on 22 variables of daily foraging trips reduced these variables to 3 principal components, which were related to diving mode (PC1), foraging effort (PC2) and variation in diving behaviour (PC3). Overall, PC1 indicated that birds from AMS dived shallower, had shorter dive duration and bottom time, and were less active during less efficient dives than birds from KER and CRO. On the other hand, PC3 showed that birds from KER segregated from those of AMS and CRO by performing more uniform foraging trips with less variability in dive parameters. The PCA emphasised that most of the characteristics of daily trips and all the characteristics of foraging dives varied according to the study sites, thus stressing the importance of distinct environments in shaping the foraging behaviour of seabirds. Food loads, and accordingly chick growth, were lower at AMS, medium at CRO and higher at KER, while indices of foraging effort presented little variation. Birds at AMS fed mainly on the euphausiid Thysanoessa gregaria and on larger juvenile squids, while birds from CRO and KER preyed upon the subantarctic krill Euphausia vallentini. Diving strategies together with food loads and chick growth rates suggest that prey availability was low at AMS, intermediate at CRO and high at KER, which is in agreement with previous data on chlorophyll concentrations and zooplankton biomass. The study shows the complexity of foraging behaviour of penguins. It illustrates the importance of behavioural plasticity and suggests that it is a fundamental trait of the life history of seabirds living in highly variable environments.
Impact of chemotherapy on postoperative complications after mastectomy and immediate breast reconstruction.

OBJECTIVES To determine the impact of chemotherapy and the timing of chemotherapy on postoperative outcomes after mastectomy and immediate breast reconstruction. DESIGN Retrospective review. SETTING University tertiary care institution. PATIENTS One hundred sixty-three consecutive patients undergoing mastectomy and immediate breast reconstruction. INTERVENTION Systemic chemotherapy for breast cancer. MAIN OUTCOME MEASURES Postoperative complications following mastectomy and immediate breast reconstruction. RESULTS One hundred sixty-three patients underwent mastectomy and immediate breast reconstruction during the study period, with a mean postoperative follow-up of 19.2 months. Sixty-six percent of the patients had expander/implant reconstruction, while 33% underwent autologous reconstruction. Fifty-seven patients received neoadjuvant chemotherapy and 41 received postoperative chemotherapy. Eighteen patients (44%) in the adjuvant chemotherapy cohort developed postoperative infections, compared with 13 patients (23%) in the neoadjuvant chemotherapy group and 16 patients (25%) who did not receive any chemotherapy (P = .05). Overall, 31% of patients had a complication requiring an unplanned return to the operating room; this rate did not differ between groups (P = .79). Of patients who underwent expander/implant reconstruction, 8 women (26%) in the neoadjuvant chemotherapy cohort, 7 women (22%) in the adjuvant chemotherapy cohort, and 8 women (18%) without chemotherapy required expander or implant removal (P = .70). CONCLUSIONS Although the highest rate of surgical site infections was in the adjuvant chemotherapy group, there were no differences between groups with respect to unplanned return to the operating room, expander loss, and donor-site complications. Neither the inclusion of chemotherapy nor the timing of its administration significantly affected the complication rates after mastectomy and immediate breast reconstruction in this population.
Home-Based Physical Activity Program Improves Depression and Anxiety in Older Adults.

BACKGROUND Late-life depression and anxiety among older adults is an important public health concern. This study examined the effect of a DVD-delivered exercise intervention on the secondary outcomes of depression and anxiety in older adults and the extent to which physical self-worth mediated the relationship between leisure-time physical activity and depression and anxiety. METHODS Older adults (N = 307) were randomized to a 6-month flexibility, toning, and balance DVD (FlexToBa™, FTB) or healthy aging DVD control. Self-reported physical activity and questionnaires were administered at baseline and postintervention. Statistical analyses were conducted in the total sample and in a subsample of participants with elevated levels of depression or anxiety. RESULTS FTB participants with elevated depression and anxiety symptoms at baseline had significantly greater reductions in depression and anxiety (d = 1.66 and 2.90) than the control condition (d = 0.77 and 0.73). The effect of physical activity on depression and anxiety was partially mediated by increases in physical self-worth in the total sample but not in those with elevated depression or anxiety. CONCLUSION A home-based physical activity intervention may be a viable treatment for reducing depression and anxiety in older adults with elevated baseline scores.