Miracle-dz/UniFAR-FTUs huggingface dataset:
Inherited genetic variation and overall survival following follicular lymphoma

Follicular lymphoma (FL) has variable progression and survival, and improved identification of patients at high risk for progression would aid in identifying patients most likely to benefit from alternative therapy.In a sample of 244 FL cases identified during a population-based case-control study of non-Hodgkin lymphoma (NHL), we examined 6,679 tag SNPs in 488 gene regions for associations with overall FL survival. Over a median follow-up of 89 months with 65 deaths in this preliminary study, we identified 5 gene regions (BMP7, GALNT12,DUSP2, GADD45B, and ADAM17) that were associated with overall survival from FL. Results did not meet the criteria for statistical significance after adjustment for multiple hypothesis testing. These results,which support a role for host factors in determining the variable progression of FL, serve as an initial examination that can inform future studies of genetic variation and FL survival. However, they require replication in independent populations, as well as assessment in rituximab-treated patients.
Embeddings from the point of view of immersion theory

Let M and N be smooth manifolds without boundary. Immersion theory suggests that an understanding of the space of smooth embeddings emb(M,N) should come from an analysis of the cofunctor V |--> emb(V,N) from the poset O of open subsets of M to spaces. We therefore abstract some of the properties of this cofunctor, and develop a suitable calculus of such cofunctors, Goodwillie style, with Taylor series and so on. The terms of the Taylor series for the cofunctor V |--> emb(V,N) are explicitly determined. In a sequel to this paper, we introduce the concept of an analytic cofunctor from O to spaces, and show that the Taylor series of an analytic cofunctor F converges to F. Deep excision theorems due to Goodwillie and Goodwillie-Klein imply that the cofunctor V |--> emb(V,N) is analytic when dim(N)-dim(M) > 2.
Cooperation and the evolution of intelligence

The high levels of intelligence seen in humans, other primates, certain cetaceans and birds remain a major puzzle for evolutionary biologists, anthropologists and psychologists. It has long been held that social interactions provide the selection pressures necessary for the evolution of advanced cognitive abilities (the ‘social intelligence hypothesis’), and in recent years decision-making in the context of cooperative social interactions has been conjectured to be of particular importance. Here we use an artificial neural network model to show that selection for efficient decision-making in cooperative dilemmas can give rise to selection pressures for greater cognitive abilities, and that intelligent strategies can themselves select for greater intelligence, leading to a Machiavellian arms race. Our results provide mechanistic support for the social intelligence hypothesis, highlight the potential importance of cooperative behaviour in the evolution of intelligence and may help us to explain the distribution of cooperation with intelligence across taxa.
Polyphenol Oxidase and o-Diphenols Inhibit Postharvest Proteolysis in Red Clover and Alfalfa

Many forages experience significant proteolytic losses when preserved by ensiling. Such losses in alfalfa (Medicago sativa L.) are especially high, with degradation of 44 to 87% of the forage protein to nonprotein N (NPN). In contrast, red clover {Trifolium pratense L. ) has up to 90% less proteolysis during ensiling. Here we demonstrate that the combination of polyphenol oxidase (PPO) and o-diphenol PPO substrates, both abundantly present in red clover, is responsible for postharvest proteolytic inhibition in this forage crop. Proteolysis in red clover leaf extracts increased nearly fivefold when endogenous o-diphenols were removed by gel filtration but returned to starting levels by adding back an exogenous o-diphenol. Proteolysis in leaf extracts of red clover plants silenced for PPO expression was dramatically increased compared to control plants. Leaf extracts of transgenic alfalfa expressing a red clover PPO gene showed a nearly fivefold o-diphenol-dependent decrease in proteolysis compared to those of control alfalfa. We also demonstrate that PPO levels 10- to 20-fold lower than those typically found in red clover are sufficient for proteolytic inhibition, that as little as 0.25 μmol o-diphenol mg -1 protein has a substantial impact on proteolysis, that a wide variety of o-diphenols are functional substrates in proteolytic inhibition, and that proteolysis is reduced for PPO-expressing alfalfa in small-scale ensiling experiments. Together, these results indicate that PPO and o-diphenols can be an effective treatment to prevent protein loss in ensiled forage crops.
Five-Year Risks of CIN 2+ and CIN 3+ Among Women With HPV-Positive and HPV-Negative LSIL Pap Results

Objective Low-grade squamous intraepithelial lesion (LSIL) Pap results do not typically lead to human papillomavirus (HPV) testing. HPV triage is not cost-effective because most cases are HPV-positive. However, under new national guidelines recommending cotesting for women aged 30 to 64 years, clinicians will increasingly receive the HPV test result with LSIL Pap results. Some authors have suggested that HPV triage might be effective at older ages, when the percentage of HPV positivity among women with LSIL declines. Methods We estimated 5-year risks of CIN 2+ and CIN 3+ among 9,033 women aged 30 to 64 years who had both an HPV test and an LSIL Pap result. Results HPV positivity among women with LSIL decreased only slightly with age (30 to 34 vs 60 to 64 years, 88% vs 72%, p < .0001). The 5-year risks of CIN 2+ and CIN 3+ of women aged 30 to 64 years testing HPV-positive/LSIL were larger than those among women testing HPV-negative/LSIL (CIN 2+, 19% vs 5.1%, p < .0001; CIN 3+, 6.1% vs 2.0%, p<.0001). The 5-year risk of CIN 3+ in HPV-negative/LSIL women was similar to that for women with atypical squamous cells of undetermined significance (ASC-US) Pap test result without knowledge of HPV test results (2.0% vs 2.6%, p = .4). Conclusions HPV-negative/LSIL posed lower risk than other Pap results that guidelines currently recommend for referral to immediate colposcopy. By the principle of “equal management of equal risks,” women with HPV-negative/LSIL might reasonably be managed similarly to those with ASC-US Pap results without knowledge of HPV testing, that is, retesting at 6 to 12 months, rather than immediate colposcopy. Although the HPV test result for LSIL Pap results provides actionable information to clinicians who screen with cotesting, the high HPV positivity of LSIL at even the oldest ages suggests the lack of cost-effectiveness of HPV triage of LSIL for clinicians who do not use routine cotesting.
Content validity of an instrument to measure young children's perceptions of the intensity of their pain.

Abstract This research article describes a study to test the content validity of the photographic scale of the Oucher, a new instrument designed to elicit children's self-reports of pain intensity. Seventy-eight 3- to 7-year-old children placed photographs of a child's face in sequence of increasing pain/hurt. The children demonstrated moderately high agreement in their consistency of the photograph sequences. The findings of the study provide support for the sequence of the photographs displayed on the Oucher and, thus, for content validity for the photographic scale.
Polyploidy in Phenotypic Space and Invasion Context: A Morphometric Study of Centaurea stoebe s.l.

The taxonomy of the Centaurea stoebe complex is controversial. Diploid and tetraploid plants occur in its native European range, but to date only tetraploids have been recorded from its introduced range in North America. We examined morphological differentiation of C. stoebe using multivariate and univariate approaches to clarify the taxonomic status of the known cytotypes. We measured more than 40 morphological traits on plants originating from 78 populations, grown from seed under uniform glasshouse conditions. The ploidy of almost 300 plants from 2 native and 20 introduced populations from Canada was assessed to test for the absence of diploids from North America. Finally, we explored whether postintroduction processes have resulted in phenotypic changes in introduced plants which may have contributed to the invasion success of C. stoebe. Morphometric analyses showed a clear separation of 2x and 4x plants and thus supported recognition of both cytotypes as separate taxa. Differences in the life cycle, the number of florets, the shape of capitula, and the shape of young rosette leaves were the best discriminant characters. Only minor differences were found between native and introduced tetraploids. All plants from the introduced range except for one hexaploid were found to be tetraploid. Rare diploids from Canada were identified as Centaurea diffusa or Centaurea psamogenna.
Modeling Familial Association of Ages at Onset of Disease in the Presence of Competing Risk

Summary In genetic family studies, ages at onset of diseases are routinely collected. Often one is interested in assessing the familial association of ages at the onset of a certain disease type. However, when a competing risk is present and is related to the disease of interest, the usual measure of association by treating the competing event as an independent censoring event is biased. We propose a bivariate model that incorporates two types of association: one is between the first event time of paired members, and the other is between the failure types given the first event time. We consider flexible measures for both types of association, and estimate the corresponding association parameters by adopting the two‐stage estimation of Shih and Louis (1995, Biometrics 51, 1384–1399) and Nan et al. (2006, Journal of the American Statistical Association 101, 65–77). The proposed method is illustrated using the kinship data from the Washington Ashkenazi Study.
Critical role of peripheral drug actions in experience‐dependent changes in nucleus accumbens glutamate release induced by intravenous cocaine

Recent studies reveal that cocaine experience results in persistent neuroadaptive changes within glutamate (Glu) synapses in brain areas associated with drug reward. However, it remains unclear whether cocaine affects Glu release in drug‐naive animals and how it is altered by drug experience. Using high‐speed amperometry with enzyme‐based and enzyme‐free biosensors in freely moving rats, we show that an initial intravenous cocaine injection at a low self‐administering dose (1 mg/kg) induces rapid, small and transient Glu release in the nucleus accumbens shell (NAc), which with subsequent injections rapidly becomes a much stronger, two‐component increase. Using cocaine‐methiodide, cocaine's analog that does not cross the blood–brain barrier, we confirm that the initial cocaine‐induced Glu release in the NAc has a peripheral neural origin. Unlike cocaine, Glu responses induced by cocaine‐methiodide rapidly habituate following repeated exposure. However, after cocaine experience this drug induces cocaine‐like Glu responses. Hence, the interoceptive actions of cocaine, which essentially precede its direct actions in the brain, play a critical role in experience‐dependent alterations in Glu release, cocaine‐induced neural sensitization and may contribute to cocaine addiction.
Performance of American Thoracic Society-recommended spirometry reference values in a multiethnic sample of adults: the multi-ethnic study of atherosclerosis (MESA) lung study.

BACKGROUND The American Thoracic Society recommends race-specific spirometric reference values from the National Health and Nutrition Survey (NHANES) III for clinical evaluation of pulmonary function in whites, African-Americans, and Mexican-Americans in the United States and a correction factor of 0.94 for Asian-Americans. We aimed to validate the NHANES III reference equations and the correction factor for Asian-Americans in an independent, multiethnic sample of US adults. METHODS The Multi-Ethnic Study of Atherosclerosis (MESA) recruited self-identified non-Hispanic white, African-American, Hispanic, and Asian-American participants aged 45 to 84 years at six US sites. The MESA-Lung Study assessed prebronchodilator spirometry among 3,893 MESA participants who performed acceptable tests, of whom 1,068 were asymptomatic healthy nonsmokers who performed acceptable spirometry. RESULTS The 1,068 participants were mean age 65 +/- 10 years, 60% female, 25% white, 20% African-American, 23% Hispanic, and 32% Asian-American. Observed values of FEV(1), FEV(6), and FVC among whites, African-Americans, and Hispanics of Mexican origin in MESA-Lung were slightly lower than predicted values based on NHANES III. Observed values among Hispanics of non-Mexican origin were consistently lower. Agreement in classification of participants with airflow obstruction based on lower limit of normal criteria was good (overall kappa = 0.88). For Asian-Americans, a correction factor of 0.88 was more accurate than 0.94. CONCLUSIONS The NHANES III reference equations are valid for use among older adults who are white, African-American, or Hispanic of Mexican origin. Comparison of white and Asian-American participants suggests that a correction factor of 0.88, applied to the predicted and lower limits of normal values, is more appropriate than the currently recommended value of 0.94.
Ontogenetic diet shifts and interrupted piscivoryin introduced largemouth bass (Micropterus salmoides)

The ecology of largemouth bass (Micropterus salmoides) is one of the best known for freshwater fish, though largely through studies within its native range (North America). I studied the habitat and diet of a bass population introduced into a Mediterranean lake. The bass displayed strong ontogenetic diet shifts as follows: young-of-the-year 300 mm, on crayfish and large fish. The diet showed several differences from most previous studies: importance of freshwater shrimp instead of insects, low piscivory, and a delay in the ontogenetic shift to piscivory. Moreover, the ontogenetic shift to piscivory was interrupted at 250‐300 mm, with consumption of shrimp and crayfish. This interruption of piscivory has been largely unreported and seems a consequence of the size-structure and species composition of the fish assemblage. A review of the literature suggests that piscivory by largemouth bass might be generally lower in populations introduced outside North America.
Single-Molecule Supercoil Relaxation Assay as a Screening Tool to Determine the Mechanism and Efficacy of Human Topoisomerase IB Inhibitors

Human nuclear type IB topoisomerase (Top1) inhibitors are widely used and powerful anticancer agents. In this study, we introduce and validate a single-molecule supercoil relaxation assay as a molecular pharmacology tool for characterizing therapeutically relevant Top1 inhibitors. Using this assay, we determined the effects on Top1 supercoil relaxation activity of four Top1 inhibitors; three clinically relevant: camptothecin, LMP-400, LMP-776 (both indenoisoquinoline derivatives), and one natural product in preclinical development, lamellarin-D. Our results demonstrate that Top1 inhibitors have two distinct effects on Top1 activity: a decrease in supercoil relaxation rate and an increase in religation inhibition. The type and magnitude of the inhibition mode depend both on the specific inhibitor and on the topology of the DNA substrate. In general, the efficacy of inhibition is significantly higher with supercoiled than with relaxed DNA substrates. Comparing single-molecule inhibition with cell growth inhibition (IC50) measurements showed a correlation between the binding time of the Top1 inhibitors and their cytotoxic efficacy, independent of the mode of inhibition. This study demonstrates that the single-molecule supercoil relaxation assay is a sensitive method to elucidate the detailed mechanisms of Top1 inhibitors and is relevant for the cellular efficacy of Top1 inhibitors. Mol Cancer Ther; 14(11); 2552–9. ©2015 AACR.
Methods in Pediatric Sleep Research and Sleep Medicine

Abstract Several methods are used to evaluate sleep in infants, children, and adolescents including: Questionnaires and diaries, actigraphy, polysomnography, and electroencephalography which are well established. Novel approaches such as high-density electroencephalography, simultaneous electroencephalography–functional magnetic resonance imaging and nonpharmacological methods aiming for a modulation of sleep are currently only used for research. These approaches might become valuable methods for clinical application in the future. The purpose of this review is to present an overview of current methods and their respective fields of application and to report available rules and recommendations for their use.
Endocytic events in TCR signaling: focus on adapters in microclusters

Summary: Although the critical role of T‐cell receptor (TCR) microclusters in T‐cell activation is now widely accepted, the mechanisms of regulation of these TCR‐rich structures, which also contain enzymes, adapters, and effectors, remain poorly defined. Soon after microcluster formation, several signaling proteins rapidly dissociate from the TCR. Recent studies from our laboratory demonstrated that the movement of the adapters linker for activation of T cells (LAT) and Src homology 2 domain‐containing leukocyte protein of 76 kDa (SLP‐76) away from initial microcluster formation sites represents endocytic events. Ubiquitylation, Cbl proteins, and multiple endocytic pathways are involved in the internalization events that disassemble signaling microclusters. Several recent studies have indicated that microcluster movement and centralization plays an important role in signal termination. We suggest that microcluster movement is directly linked to endocytic events, thus implicating endocytosis of microclusters as a means to regulate signaling output of the T cell.
Charge Carrier Dynamics in Organometal Halide Perovskite Probed by Time-Resolved Electrical Measurements

This chapter presents the fate of the charge carriers from the moment of its photogenera‐ tion in the perovskite to injection and transport into electrodes. Time-resolved electrical measurement techniques, terahertz (THz) spectroscopy and microwave (MW) conductiv‐ ity, are primarily used to deconvolute ultrafast processes and to directly access behavior of charged species from the ps to µs timescales. Transient absorption and photolumines‐ cence spectroscopy were also utilized to gain insight on carrier population dynamics and radiatively recombining charges. Photogenerated charged species were converted into highly mobile charges (µ e = 12.5 cm 2 V -1 s -1 and µ h = 7.5 cm 2 V -1 s -1 ) almost instantaneously (< 0.2 ps), while the remaining loosely bounded excitons dissociate into mobile charges after 2-3 ps. This high mobility is maintained for at least 1 ns as obtained by THz spectroscopy, while its lifetime is at least few tens of µs as measured by the MW conductivity techni‐ que. Lowering the temperature increases carrier mobilities with T -1.6 . Dependence and a 75 meV barrier energy is required for temperature-activated recombination. Finally, injec‐ tion of hole from MAPbI 3 to Spiro-OMeTAD was found to be ultrafast and the state and population of dark holes dictate its recombination. mobility and its population occurs on a timescale longer than 1 µs, as shown by TRMC traces. Moreover, this means that charges can move over large distances allowing them to be extracted at the electrodes. As a summary of this section, the combination of several time-resolved spectroscopy techni‐ ques, i.e., optical transient absorption, TRTS, and TRMC, characterization of the charge carrier dynamics in neat MAPbI 3, and MAPbI 3 attached with TiO 2 and Al 2 O 3 was presented. Thin film of perovskite and that attached to Al 2 O 3 have properties of an ideal solar cell device: Electron and holes are formed in sub-ps timescale with very high mobilities. Its estimated values suggest that they are almost balanced and carriers do not recombine until after tens of microseconds. These characteristics almost guarantee efficient charge collection, a very desirable property of solar cell device. Electron injection to TiO 2 lowers electron mobility resulting to unbalanced charge transport that could lead to built-in electric field. Engineering of electrodes such that balanced transport is still achieved is one possible way of improving its overall power conversion efficiency. MAPbI Fig.10b, TRMC excitation MAPbI fluences 11 2 second-order recombination. bilayer for MAPbI 3 /PCBM, for 12
A Study on Interpersonal Forgive and Revenge of Undergraduates and their Links with Depression

To explore the relationship between interpersonal forgive and revenge and their effects on depression in college students,A Rumination Scale, Tendency to Forgive Scale, Revenge Motivation Scale, Attitude Toward Forgiveness Scale and Center for Epidemiologic Studies Depression Scale were administered to 236 sophomores. Results and Conclusion: (1) There were significant gender differences in the degree of seeking revenge. (2) Correlation analysis showed significantly negative correlation between tendency to forgive and revenge motivations as well as rumination,;Correlation analysis also showed significantly positive correlation between rumination and depression. (3) Regression analysis revealed that rumination were significant positive predictors of depression; tendency to forgive were significant negative predictors of depression. (4) Regression analysis also revealed that the TTF/ATF interaction and TTF/Revenge interaction were not significant predictors of depression.
Global meta‐analysis of native and nonindigenous trophic traits in aquatic ecosystems

Ecologists have recently devoted their attention to the study of species traits and their role in the establishment and spread of nonindigenous species (NIS). However, research efforts have mostly focused on studies of terrestrial taxa, with lesser attention being dedicated to aquatic species. Aquatic habitats comprise of interconnected waterways, as well as exclusive introduction vectors that allow unparalleled artificial transport of species and their propagules. Consequently, species traits that commonly facilitate biological invasions in terrestrial systems may not be as represented in aquatic environments. We provide a global meta‐analysis of studies conducted in both marine and freshwater habitats. We selected studies that conducted experiments with native and NIS under common environmental conditions to allow detailed comparisons among species traits. In addition, we explored whether different factors such as species relatedness, functional feeding groups, latitude, climate, and experimental conditions could be linked to predictive traits. Our results show that species with traits that enhance consumption and growth have a substantially increased probability of establishing and spreading when entering novel ecosystems. Moreover, traits associated with predatory avoidance were more prevalent in NIS and therefore favour invasive species in aquatic habitats. When we analysed NIS interacting with taxonomically distinctive native taxa, we found that consumption and growth were particularly important traits. This suggests that particular attention should be paid to newly introduced species for which there are no close relatives in the local biota. Finally, we found a bias towards studies conducted in temperate regions, and thus, more studies in other climatic regions are needed. We conclude that studies aiming at predicting future range shifts should consider trophic traits of aquatic NIS as these traits are indicative of multiple interacting mechanisms involved in promoting species invasions.