Miracle-dz/UniFAR-FTUs huggingface dataset:
A Generalized Moments Specification Test of the Proportional Hazards Model

Abstract This article describes a generalized moments specification test of the semiparametric proportional hazards model of Cox. In contrast to other specification tests for this model, the generalized moments test is applicable in the presence of continuous explanatory variables and does not require assigning the data to predetermined cells. The results of a Monte Carlo investigation suggest that the generalized moments test has good finite-sample properties and that it is more powerful than other available tests for models with continuous explanatory variables when the alternative is an accelerated failure time model. The test is based on generalized residuals for the proportional hazards model. When the model is correct, the generalized residuals have asymptotically the (possibly censored) unit exponential distribution. The generalized moments are means of functions of the generalized residuals. The generalized moments have known values when the generalized residuals have the unit exponential distribu.
Experimental demonstration of an acoustic time reversal mirror in the ocean

A time‐reversal mirror (TRM) was implemented in an experiment conducted in the Mediterranean Sea in April 1996. The experiment utilized a vertical source–receiver array (SRA) spanning 77 m of a 125‐m water column with 20 sources and receivers and a single source/receiver transponder (SRT) colocated in range with another vertical receive array (VRA) of 46 elements spanning 90 m of a 145‐m water column located 6.3 km from the SRA. The TRM demonstration consisted of transmitting a 50‐ms pulse from the SRT to the SRA, digitizing the received signal, and retransmitting the time‐reversed signals from all the sources of the SRA. The retransmitted signal was then received at the VRA. An assortment of runs were made to examine the structure of the focal point region and the temporal stability of the process. The process was extremely robust and stable. Iterative enhancement of the focusing process was also demonstrated by a ‘‘ping‐pong’’ exchange of a pulse between the transponder and the TRM.
Evidence for isotropic fractionation of carbon monoxide in dark clouds

Chemical fractionation of the various isotopes of carbon mmonoxide has been studied in four isolated dark clouds. At positions away from the centers of three of the objects: B5, B335, and L1262: the abundance of /sup 13/CO relative to C/sup 18/O is at least a factor of 4 greater than at the central positions. This detection of carbon isotope fractionation is consistent with theoretical predictions of /sup 13/CO enhancement in the outer parts of cool clouds. Combined observations of the J=2. -->. 1 and J=1. -->. 0 transitions of several CO isotopes have enabled us to derive molecular hydrogen densities and to assess the effect of saturation and resonant scattering. Abundance ratios of the rarer isotopic species in the cloud centers have also been determined.
Polygenic adaptation dynamics in large, finite populations

Although many phenotypic traits are determined by a large number of genetic variants, how a polygenic trait adapts in response to a change in the environment is not completely understood. In the framework of diffusion theory, we study the steady state and the adaptation dynamics of a large but finite population evolving under stabilizing selection and symmetric mutations when selection and mutation are moderately large. We find that in the stationary state, the allele frequency distribution at a locus is unimodal if its effect size is below a threshold effect and bimodal otherwise; these results are the stochastic analog of the deterministic ones where the stable allele frequency becomes bistable when the effect size exceeds a threshold. It is known that following a sudden shift in the phenotypic optimum, in an infinitely large population, selective sweeps at a large-effect locus are prevented and adaptation proceeds exclusively via subtle changes in the allele frequency; in contrast, we find that the chance of sweep is substantially enhanced in large, finite populations and the allele frequency at a large-effect locus can reach a high frequency at short times even for small shifts in the phenotypic optimum.
Statistical evaluation of character support reveals the instability of higher-level dinosaur phylogeny

The interrelationships of the three major dinosaur clades (Theropoda, Sauropodomorpha, and Ornithischia) have come under increased scrutiny following the recovery of conflicting phylogenies by a large new character matrix and its extensively modified revision. Here, we use tools derived from recent phylogenomic studies to investigate the strength and causes of this conflict. Using maximum likelihood as an overarching framework, we examine the global support for alternative hypotheses as well as the distribution of phylogenetic signal among individual characters in both the original and rescored dataset. We find the three possible ways of resolving the relationships among the main dinosaur lineages (Saurischia, Ornithischiformes, and Ornithoscelida) to be statistically indistinguishable and supported by nearly equal numbers of characters in both matrices. While the changes made to the revised matrix increased the mean phylogenetic signal of individual characters, this amplified rather than reduced their conflict, resulting in greater sensitivity to character removal or coding changes and little overall improvement in the ability to discriminate between alternative topologies. We conclude that early dinosaur relationships are unlikely to be resolved without fundamental changes to both the quality of available datasets and the techniques used to analyze them.
Structure of the Commander endosomal trafficking complex linked to X-linked intellectual disability/Ritscher-Schinzel syndrome

The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two subassemblies; Retriever composed of VPS35L, VPS26C and VPS29, and the CCC complex which contains ten subunits COMMD1-COMMD10 and two coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy and in silico predictions we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilised by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a sixteenth subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.
Molecular Jackhammers Eradicate Cancer Cells by Vibronic-Driven Action

Through the actuation of vibronic modes in cell-membrane-associated aminocyanines, a new type of molecular mechanical action can be exploited to rapidly kill cells by necrosis. This is done using near-infrared light, a low energy source hitherto thought to be insufficient to permit molecular mechanical disruption of a cell membrane. Vibronic-driven action (VDA) is distinct from both photodynamic therapy and photothermal therapy in that the VDA mechanical effect on the cell membrane is not retarded by high doses of inhibitors of reactive oxygen species (ROS), and VDA does not itself induce an increase in the temperature of the media; it is also unaffected by cooling the media to 2 °C. The picosecond concerted whole-molecule-vibrations of VDA-induced mechanical disruption can be done with very low concentrations (500 nM) of the aminocyanines or low doses of light (12 Jcm-2, 80 mWcm-2 for 2.5 min) to cause in vitro necrotic cell death in >99% of human melanoma cells. The effect is also studied in vivo in murine B16-F10 and human A375 melanoma in mice, underscoring the high efficiency of this approach, achieving a survival rate of 60% at day 120, and 50% of the mice becoming tumor free. The molecules that destroy cell membranes through VDA are termed molecular jackhammers (MJH) because they undergo concerted whole-molecule vibrations. Different than traditional chemotherapy, it is unlikely that a cell could develop a resistance to molecular mechanical forces, thereby providing a new modality for inducing cancer cell death.
A Practical Template Attack on CRYSTALS-Dilithium

This paper presents a new profiling side-channel attack on the signature scheme CRYSTALS-Dilithium, which has been selected by the NIST as the new primary standard for quantum-safe digital signatures. This algorithm has a constant-time implementation with consideration for side-channel resilience. However, it does not protect against attacks that exploit intermediate data leakage. We exploit such a leakage on a vector generated during the signing process and whose costly protection by masking is a matter of debate. We design a template attack that enables us to efficiently predict whether a given coefficient in one coordinate of this vector is zero or not. Once this value has been completely reconstructed, one can recover, using linear algebra methods, part of the secret key that is sufficient to produce universal forgeries. While our paper deeply discusses the theoretical attack path, it also demonstrates the validity of the assumption regarding the required leakage model, from practical experiments with the reference implementation on an ARM Cortex-M4.
A Test for Structural Stability of Euler Conditions Parameters Estimated Via the Generalized Methods of Moments Estimators

Un Test de la Stabilite Structurelle des Parametres Estimee Par la Methode des Moments Generalisee (Mmg) Est Presente. le Test Est Predictif, Base Sur L'examen de Previsions Sur un Sous-Echantillon le Test S'applique Sur une Grande Variete de Modeles D'inference Dynamiques, Modeles D'equations Simultanees Non-Lineaires Pour une Large Classe de Methodes D'inference Couverte Par L'estimateur Mmg. les Proprietes Asymptotiques et L'efficacite Locale Sont Derivees. Il Est Demontre Que le Test a une Efficacite Asymptotique Equivalente Pour des Alternatives Locales Dans Chaque Sous-Echantillon, Quel Que Soit Celui Qui Etait Conditionnel a L'autre. le Test a Plusieurs Avantages Particulierement Importants Pour les Modeles Dynamiques Non-Lineaires.
Immune responses in mildly versus critically ill COVID-19 patients

The current coronavirus pandemic (COVID-19), caused by SARS-CoV-2, has had devastating effects on the global health and economic system. The cellular and molecular mediators of both the innate and adaptive immune systems are critical in controlling SARS-CoV-2 infections. However, dysregulated inflammatory responses and imbalanced adaptive immunity may contribute to tissue destruction and pathogenesis of the disease. Important mechanisms in severe forms of COVID-19 include overproduction of inflammatory cytokines, impairment of type I IFN response, overactivation of neutrophils and macrophages, decreased frequencies of DC cells, NK cells and ILCs, complement activation, lymphopenia, Th1 and Treg hypoactivation, Th2 and Th17 hyperactivation, as well as decreased clonal diversity and dysregulated B lymphocyte function. Given the relationship between disease severity and an imbalanced immune system, scientists have been led to manipulate the immune system as a therapeutic approach. For example, anti-cytokine, cell, and IVIG therapies have received attention in the treatment of severe COVID-19. In this review, the role of immunity in the development and progression of COVID-19 is discussed, focusing on molecular and cellular aspects of the immune system in mild vs. severe forms of the disease. Moreover, some immune- based therapeutic approaches to COVID-19 are being investigated. Understanding key processes involved in the disease progression is critical in developing therapeutic agents and optimizing related strategies.
Sex hormone influence on female-biased autoimmune diseases hints at puberty as an important factor in pathogenesis

The majority of autoimmune diseases affect more women than men, suggesting an important role for sex hormones in regulating immune response. Current research supports this idea, highlighting the importance of sex hormones in both immune and metabolic regulation. Puberty is characterized by drastic changes in sex hormone levels and metabolism. These pubertal changes may be what forms the gulf between men and women in sex bias towards autoimmunity. In this review, a current perspective on pubertal immunometabolic changes and their impact on the pathogenesis of a select group of autoimmune diseases is presented. SLE, RA, JIA, SS, and ATD were focused on in this review for their notable sex bias and prevalence. Due to both the scarcity of pubertal autoimmune data and the differences in mechanism or age-of-onset in juvenile analogues often beginning prior to pubertal changes, data on the connection between the specific adult autoimmune diseases and puberty often relies on sex hormone influence in pathogenesis and established sex differences in immunity that begin during puberty.
Structural change in feedlot cattle death loss rates

Introduction Industry reports and anecdotal evidence indicate that the death loss rate in cattle feedlots has increased over time. Such increases in death loss rates impact feedlot cost and thus profitability. Objectives The primary objective of this study is to examine whether feedlot death loss rates in cattle have changed over time, to analyze the nature of any identified structural change, and to identify possible catalysts for that change. Methods Data from the Kansas Feedlot Performance and Feed Cost Summary from 1992 through 2017 is used to model feedlot death loss rate as a function of feeder cattle placement weight, days on feed, time, and seasonality in the form of monthly dummy variables. Commonly used tests of structural change, including the CUSUM, CUSUMSQ, and Bai and Perron methods, are implemented to examine the existence and nature of any structural changes in the proposed model. All tests indicate the presence of structural breaks in the model, including both systematic change and abrupt change. Following a synthesis of structural test results, the final model is modified to include a structural shift parameter for the period from December 2000 to September 2010. Results Models indicate that days on feed has a significant positive influence on death loss rate. Trend variables indicate that death loss rates have increased systematically over the period studied. However, the structural shift parameter in the modified model is positive and significant for December 2000 to September 2010, indicating that death loss is higher on average during this period. Variance of death loss percentage is also higher during this period. Parallels between evidence of structural change and possible industry and environmental catalysts are also discussed. Conclusions Statistical evidence does indicate changes in the structure of death loss rates. Ongoing factors such as changes in feeding rations prompted by market forces and feeding technologies may have contributed to systematic change. Other events, such as weather events and beta agonist use could result in abrupt changes. No clear evidence directly connects these factors to death loss rates and disaggregated data would be required to facilitate such a study.
Publications of the Astronomical Society of the Pacific 99: 1127-1133, November 1987 THE LONG-PERIOD VARIABLE STARS OF M 33*

Infrared photometry of long-period variables in M 33 shows that the majority of those identified up to now are supergiants. The tip of the asymptotic giant branch may also be visible, but the present data are not adequate to decide the matter. Calibration photometry presented here confirms that the distance of M 33 is 890 kpc with an uncertainty of approximately 15%. The Cepheid and supergiant period-luminosity relations are in satisfactory agreement on this point.
C:N:P stoichiometric variations of herbs and its relationships with soil properties and species relative abundance along the Xiaokai River irrigation in the Yellow River Delta, China

Introduction Soil salinity is known to affect plant performance and nutrient stoichiometry by altering their ecophysiology, and thus playing a crucial role in determining plant distribution patterns and nutrient cycles in salinized ecosystems. However, there was little consensus on the effects of salinity stress on plant C, N, and P stoichiometries. Moreover, determining the relationships between species relative species abundance and plant C, N, and P stoichiometries can help to understand the different adaptive strategies between the common and rare species as well as the community assembly process. Methods We determined the plant C, N, P stoichiometries at the community and species levels and the relative abundance of species as well as the corresponding soil properties from five sampling sites along a soil salinity gradient in the Yellow River Delta, China. Results and Discussion We found that the C concentration of belowground part increased with soil salinity. Meanwhile, plant community N concentration and C:N ratio tended to decrease with soil salinity, whereas the P concentration, C:P, and N:P ratios exhibited the opposite trends. This indicated that N use efficiency increased, while P use efficiency decreased with soil salinity. Moreover, the decreased N:P ratio indicated that N limitation was gradually aggravated along the soil salinity gradient. The soil C:P ratio and P concentration were the major factors of plant C, N, and P stoichiometries in the early growth stage, whereas the soil pH and P concentration were the major factors of plant C, N, and P stoichiometries in the late growth stage. Compared with that of the rare species, the C:N:P stoichiometry of the most common species was medium. Moreover, the intraspecific variations in the aboveground part N:P ratio and belowground part C concentration showed a significant correlation with species’ relative abundance, which indicated that higher intraspecific trait variation might facilitate greater fitness and survival opportunities in environments with high heterogeneity. Conclusion Our results revealed that the plant community C:N:P stoichiometry and its determining soil properties varied with plant tissues as well as sampling seasons, and emphasized the importance of intraspecific variation in determining the functional response of plant communities to salinity stress.
Application of machine learning algorithms for prediction of ultraviolet absorption spectra of chromophoric dissolved organic matter (CDOM) in seawater

The ultraviolet absorption spectra of chromophoric dissolved organic matter (CDOM) can be used to trace its sources and to explore the dynamic of the CDOM pool. In previous studies, only the spectra above 240 nm can be used directly to characterize the CDOM in seawater, due to the overlapping of CDOM absorption spectra below 240 nm with inorganic chemicals such as NO 3 − , NO 2 − , Cl- and Br-. In this study, three different machine learning models, back propagation neural network (BPNN), random forest (RF) and extreme gradient boosting (XGBoost), were built to predict the CDOM ultraviolet absorption spectra between 215 and 350 nm after being trained with the raw absorption spectra of seawater. The optimal input wavelength range of the raw seawater spectra is 250-350 nm, and the optimal model parameters of machine learning algorithms were determined by using five-fold cross validation. The results show that the three models can well predict the CDOM absorption spectra. Comparatively, the XGBoost model gave the best prediction results. The reasons might be related to the fact that the XGBoost algorithm focuses on the residuals generated by the last iteration, which can reduce both variance and bias, especially for datasets with small sample sizes. Based on the predicted spectra by XGBoost algorithm, we calculated the spectra slopes of short wavelengths between 215 and 240 nm (S215-240) and between 215 and 275 nm (S215-275). The results show that the S215-240 and S215-275 are ~2 times the widely used spectra slopes between 275 and 295 nm (S275-295) obtained by traditional method based on the raw spectra. Moreover, the S215-240 and S215-275 are more relavant with salinity for marine CDOM than S275-295, suggesting spectra slopes of shorter wavelengths might be the better proxies for marine CDOM than that of longer wavelengths.
Beat alignment ability is associated with formal musical training not current music playing

The ability to perceive the beat in music is crucial for both music listeners and players with expert musicians being notably skilled at noticing fine deviations in the beat. However, it is unclear whether this beat perception ability is enhanced in trained musicians who continue to practice relative to musicians who no longer play. Thus, we investigated this by comparing active musicians’, inactive musicians’, and nonmusicians’ beat alignment ability scores on the Computerized Adaptive Beat Alignment Test (CA-BAT). 97 adults with diverse musical experience participated in the study, reporting their years of formal musical training, number of instruments played, hours of weekly music playing, and hours of weekly music listening, in addition to their demographic information. While initial tests between groups indicated active musicians outperformed inactive musicians and nonmusicians on the CA-BAT, a generalized linear regression analysis showed that there was no significant difference once differences in musical training had been accounted for. To ensure that our results were not impacted by multicollinearity between music-related variables, nonparametric and nonlinear machine learning regressions were employed and confirmed that years of formal musical training was the only significant predictor of beat alignment ability. These results suggest that expertly perceiving fine differences in the beat is not a use-dependent ability that degrades without regular maintenance through practice or musical engagement. Instead, better beat alignment appears to be associated with more musical training regardless of continued use.
Cervical lymphadenopathy as initial presentation of metastatic prostate cancer: A retrospective study of five cases and literature review

Cervical lymphadenopathy as the initial presentation of metastatic prostate cancer is particularly uncommon, and easily misdiagnosed. In the current study, we describe five cases of metastatic prostate cancer in our hospital that presented with cervical lymphadenopathy as an initial symptom. The diagnosis was confirmed by needle biopsy of the suspicious lymph nodes and the serum prostate specific antigen (PSA) levels of all patients exceeded 100 ng/ml. The five patients were treated with hormonal therapy; four received traditional hormonal therapy, including bicalutamide and goserelin; one patient received hormonal therapy that included abiraterone and goserelin. Case 1 developed into castration-resistant prostate cancer (CRPC) after 7 months and died after 12 months. Case 2 rejected regular hormonal therapy for personal reasons and died 6 months after the initial diagnosis. Case 3 was still alive at the time of writing. Case 4 was administered with abiraterone, prednisolone and goserelin; the treatment was effective and the patient has remained symptom-free for the last 24 months. Case 5 was treated with hormonal and chemotherapy but died 8 months after diagnosis. In conclusion, any elderly male presenting with cervical lymphadenopathy should be considered the possibility of prostate cancer, especially when the needle biopsy reveals adenocarcinoma. The prognosis for patients presented with cervical lymphadenopathy as the initial presentation is usually poor. Hormone therapy based on abiraterone may yield a better response in such cases.