Miracle-dz/UniFAR-FTUs huggingface dataset:
Homeostatic responses regulate selfish mitochondrial genome dynamics in C. elegans

Selfish genetic elements have profound biological and evolutionary consequences. Mutant mitochondrial genomes (mtDNA) can be viewed as selfish genetic elements that persist in a state of heteroplasmy despite having potentially deleterious consequences to the organism. We sought to investigate mechanisms that allow selfish mtDNA to achieve and sustain high levels. Here, we establish a large 3.1kb deletion bearing mtDNA variant uaDf5 as a bona fide selfish genome in the nematode Caenorhabditis elegans. Next, using droplet digital PCR to quantify mtDNA copy number, we show that uaDf5 mutant mtDNA replicates in addition to, not at the expense of, wildtype mtDNA. These data suggest existence of homeostatic copy number control for wildtype mtDNA that is exploited by uaDf5 to ‘hitchhike’ to high frequency. We also observe activation of the mitochondrial unfolded protein response (UPRmt) in animals with uaDf5. Loss of UPRmt results in a decrease in uaDf5 frequency whereas constitutive activation of UPRmt increases uaDf5 levels. These data suggest that UPRmt allows uaDf5 levels to increase. Interestingly, the decreased uaDf5 levels in absence of UPRmt recover in parkin mutants lacking mitophagy, suggesting that UPRmt protects uaDf5 from mitophagy. We propose that cells activate two homeostatic responses, mtDNA copy number control and UPRmt, in uaDf5 heteroplasmic animals. Inadvertently, these homeostatic responses allow uaDf5 levels to be higher than they would be otherwise. In conclusion, our data suggest that homeostatic stress response mechanisms play an important role in regulating selfish mitochondrial genome dynamics.
Statistical Learning Is Related to Reading Ability in Children and Adults

There is little empirical evidence showing a direct link between a capacity for statistical learning (SL) and proficiency with natural language. Moreover, discussion of the role of SL in language acquisition has seldom focused on literacy development. Our study addressed these issues by investigating the relationship between SL and reading ability in typically developing children and healthy adults. We tested SL using visually presented stimuli within a triplet learning paradigm and examined reading ability by administering the Wide Range Achievement Test (WRAT-4; Wilkinson & Robertson, 2006). A total of 38 typically developing children (mean age of 9;5 years, range 6;4-12;5) and 37 healthy adults (mean age of 21 years, range 18-34) were assessed. In children, SL was significantly related to reading ability. Importantly, this relationship was independent of grade and also age. The adult data, too, revealed that SL was significantly related to reading ability. A regression analysis of the combined child and adult data revealed that SL accounted for a unique amount of variance in reading ability, after age and attention had been taken into consideration. For the first time, this study provides empirical evidence that a capacity for more effective SL is related to higher reading ability in the general population.
Cortex mapping reveals regionally specific patterns of genetic and disease-specific gray-matter deficits in twins discordant for schizophrenia

The symptoms of schizophrenia imply disruption to brain systems supporting higher-order cognitive activity, but whether these systems are impacted differentially against a background of diffuse cortical gray-matter deficit remains ambiguous. Some unaffected first-degree relatives of schizophrenics also manifest cortical gray-matter deficits, but it is unclear whether these changes are isomorphic with those in patients, and the answer is critical to understanding the neurobiological conditions necessary for disease expression given a predisposing genotype. Here we report three-dimensional cortical surface maps (probabilistic atlases matching subjects' anatomy point by point throughout cortex) in monozygotic (MZ) and dizygotic (DZ) twins discordant for chronic schizophrenia along with demographically matched control twins. A map encoding the average differences between schizophrenia patients and their unaffected MZ co-twins revealed deficits primarily in dorsolateral prefrontal cortex, superior temporal gyrus, and superior parietal lobule. A map encoding variation associated with genetic proximity to a patient (MZ co-twins > DZ co-twins > control twins) isolated deficits primarily in polar and dorsolateral prefrontal cortex. In each case, the statistical significance was confirmed through analysis of 10,000 Monte Carlo permutations, and the remaining cortex was shown to be significantly less affected by contrast analysis. The disease-related deficits in gray matter were correlated with measures of symptom severity and cognitive dysfunction but not with duration of illness or antipsychotic drug treatment. Genetic and disease-specific influences thus affect gray matter in partially nonoverlapping areas of predominantly heteromodal association cortex, changes that may act synergistically in producing overt behavioral features of the disorder.
Rumen Degradability and Post-ruminal Digestion of Dry Matter, Nitrogen and Amino Acids of Three Protein Supplements

This study evaluated the in situ ruminal degradability, and subsequent small intestinal digestibility (SID) of dry matter, crude protein (CP), and amino acids (AA) of cottonseed meal (CSM), sunflower seed meal (SFSM) and distillers dried grains with solubles (DDGS) by using the modified three-step in vitro procedure. The ruminal degradability and subsequent SID of AA in rumen-undegradable protein (RUP-AA) varied among three protein supplements. The result show that the effective degradability of DM for SFSM, CSM, and DDGS was 60.8%, 56.4%, and 41.0% and their ruminal fermentable organic matter was 60.0%, 55.9%, and 39.9%, respectively. The ruminal degradable protein (RDP) content in CP for SFSM, CSM, and DDGS was 68.3%, 39.0%, and 32.9%, respectively, at the ruminal solid passage rate of 1.84%/h. The SFSM is a good source of RDP for rumen micro-organisms; however, the SID of RUP of SFSM was lower. The DDGS and CSM are good sources of RUP for lambs to digest in the small intestine to complement ruminal microbial AA of growing lambs. Individual RUP-AA from each protein source was selectively removed by the rumen micro-organisms, especially for Trp, Arg, His, and Lys (p<0.01). The SID of individual RUP-AA was different within specific RUP origin (p<0.01). Limiting amino acid was Leu for RUP of CSM and Lys for both RUP of SFSM and DDGS, respectively. Therefore, different protein supplements with specific limitations should be selected and combined carefully in growing lambs ration to optimize AA balance.
Analysis of the dynamics of adaptation to transgenic corn and crop rotation by western corn rootworm (Coleoptera: Chrysomelidae) using a daily time-step model.

Western corn rootworm, Diabrotica virgifera virgifera LeConte, has overcome crop rotation in several areas of the north central United States. The effectiveness of crop rotation for management of corn rootworm has begun to fail in many areas of the midwestern United States, thus new management strategies need to be developed to control rotation-resistant populations. Transgenic corn, Zea mays L. , effective against western corn rootworm, may be the most effective new technology for control of this pest in areas with or without populations adapted to crop rotation. We expanded a simulation model of the population dynamics and genetics of the western corn rootworm for a landscape of corn; soybean, Glycine max (L.); and other crops to study the simultaneous development of resistance to both crop rotation and transgenic corn. Results indicate that planting transgenic corn to first-year cornfields is a robust strategy to prevent resistance to both crop rotation and transgenic corn in areas where rotation-resistant populations are currently a problem or may be a problem in the future. In these areas, planting transgenic corn only in continuous cornfields is not an effective strategy to prevent resistance to either trait. In areas without rotation-resistant populations, gene expression of the allele for resistance to transgenic corn, R, is the most important factor affecting the evolution of resistance. If R is recessive, resistance can be delayed longer than 15 yr. If R is dominant, resistance may be difficult to prevent. In a sensitivity analysis, results indicate that density dependence, rotational level in the landscape, and initial allele frequency are the three most important factors affecting the results.
A Sharp Tail Bound for the Expander Random Sampler

Consider an expander graph in which a $\mu$ fraction of the vertices are marked. A random walk starts at a uniform vertex and at each step continues to a random neighbor. Gillman showed in 1993 that the number of marked vertices seen in a random walk of length $n$ is concentrated around its expectation, $\Phi := \mu n$, independent of the size of the graph. Here we provide a new and sharp tail bound, improving on the existing bounds whenever $\mu$ is not too large.
Prevalence of social-emotional and behavioral problems in a community sample of 1- and 2-year-old children.

OBJECTIVE To examine the prevalence of infant-toddler social-emotional and behavioral problems and associations with social-emotional competence, interference in family life, and parental worry. METHOD The sample consisted of 1- and 2-year-old children (mean [MN] age = 24.8 months) from the baseline survey of a representative sample of healthy births (N= 1,280). Parent questionnaires included the Child Behavior Checklist (CBCL/2-3), Parenting Stress Index Short Form (PSI/SF), and Infant-Toddler Social and Emotional Assessment social-emotional competence scales, as well as questions about parental worry and family activities. RESULTS Approximately 80% of eligible subjects participated. The weighted prevalence of parent-reported subclinical/clinical CBCL/2-3 scores was 11.8% for 2-year-olds. Approximately 6% of parents of 1- and 2-year-olds reported clinical-level scores on the PSI Difficult Child (PSI/DC) scale, which was included as a proxy for behavior problems among 1-year-olds, for whom measures were limited. Sex differences were not observed. CBCL/2-3 and PSI/DC scores were uniquely associated with economic disadvantage (relative risk = 1.89 and 2.24, respectively). Approximately 32% of 2-year-olds with subclinical/clinical CBCL2-3 scores had delayed social-emotional competence. Problems were also associated with parental worry about child behavior and interference in family activities. CONCLUSIONS A significant need for early identification of emotional/behavioral problems in very young children is highlighted by associations with delayed competence and disruptions in family life that may further contribute to risk for persistent problems.
Large covariance estimation by thresholding principal orthogonal complements

The paper deals with the estimation of a high dimensional covariance with a conditional sparsity structure and fast diverging eigenvalues. By assuming a sparse error covariance matrix in an approximate factor model, we allow for the presence of some cross‐sectional correlation even after taking out common but unobservable factors. We introduce the principal orthogonal complement thresholding method ‘POET’ to explore such an approximate factor structure with sparsity. The POET‐estimator includes the sample covariance matrix, the factor‐based covariance matrix, the thresholding estimator and the adaptive thresholding estimator as specific examples. We provide mathematical insights when the factor analysis is approximately the same as the principal component analysis for high dimensional data. The rates of convergence of the sparse residual covariance matrix and the conditional sparse covariance matrix are studied under various norms. It is shown that the effect of estimating the unknown factors vanishes as the dimensionality increases. The uniform rates of convergence for the unobserved factors and their factor loadings are derived. The asymptotic results are also verified by extensive simulation studies. Finally, a real data application on portfolio allocation is presented.
ANTIGENS IN EGGS AND DEVELOPMENTAL STAGES OF THE SEA URCHIN

A number of antigens in unfertilized eggs and embryos of the sea urchin Paracentrotus lividus were characterized with respect to both immunological and physicochemical properties. Experiments involved single diffusion in agar (Oudin technique) combined with mutual dilution, serial dilution, and heating of antigenic extracts, as well as immunoelectrophoresis with normal and heated extracts and agar electrophoresis followed by staining of the antigenic spots with protein specific dyes. The gradual transition in migration rates of bands of precipitates in Oudin tubes following mutual dilution of either extracts or antisera allowed the identification of 6 immunologically identical antigens in eggs and embryonic stages. Similarities with respect to diffusion coefficients, sensitivity to heat, electrophoretic mobility, and reaction to protein specific dyes indicated that the antigens in extracts of eggs and various developmental stages also had certain physicochemical properties in common. Such knowledge is of importance for an understanding of antigenic changes occurring during ontogenesis.
Comprehension of Pictorial Symbols: Effects of Context and Test Method

This research examined two factors involved in the evaluation of pictorial symbol comprehension: context (absence vs. presence of photographs depicting the probable environments where a symbol would be seen) and test method (multiple-choice with less vs. more plausible distractor alternatives vs. open-ended). We tested 33 pictorial symbols from various sources. The results showed that the multiple-choice test with less plausible distractors inflated comprehension scores by an average of 30% compared with the other two tests, which did not differ. The presence of context increased symbol comprehension in the open-ended test and in the multiple-choice test that had more plausible distractors. Extensive preliminary procedures demonstrated the difficulty of forming a multiple-choice test with plausible distractor alternatives. This fact, combined with multiple-choice tests′ low ecological validity in reflecting the real-world task of symbol comprehension, suggests that this test should be avoided in favor of an open-ended testing procedure. It is suggested that context provides ecologically valid cues that limit the range of possible constructs that the pictorial symbol could be, raising comprehension scores. The use of context may help reduce the costs (money, time, effort) of producing pictorial symbols with acceptable, above-criterion comprehension levels.
Spindle checkpoint deficiency is tolerated by murine epidermal cells but not hair follicle stem cells

The spindle assembly checkpoint (SAC) ensures correct chromosome segregation during mitosis by preventing aneuploidy, an event that is detrimental to the fitness and survival of normal cells but oncogenic in tumor cells. Deletion of SAC genes is incompatible with early mouse development, and RNAi-mediated depletion of SAC components in cultured cells results in rapid death. Here we describe the use of a conditional KO of mouse Mad2, an essential component of the SAC signaling cascade, as a means to selectively induce chromosome instability and aneuploidy in the epidermis of the skin. We observe that SAC inactivation is tolerated by interfollicular epidermal cells but results in depletion of hair follicle bulge stem cells. Eventually, a histologically normal epidermis develops within ∼1 mo after birth, albeit without any hair. Mad2-deficient cells in this epidermis exhibited abnormal transcription of metabolic genes, consistent with aneuploid cell state. Hair follicle bulge stem cells were completely absent, despite the continued presence of rudimentary hair follicles. These data demonstrate that different cell lineages within a single tissue respond differently to chromosome instability: some proliferating cell lineages can survive, but stem cells are highly sensitive.
Likelihood ratio based mixed resolution facial comparison

In this paper, we propose a novel method for low-resolution face recognition. It is especially useful for a common situation in forensic search where faces of low resolution, e.g. on surveillance footage or in a crowd, must be compared to a high-resolution reference. This method is based on the likelihood ratio of a pair of mixed-resolution input images. The effectiveness of our method is tested on the SCface database which contains face images taken by surveillance cameras. The results show that our method outperforms recently published state-of-the-art.
Metallothionein and apoptosis in primary human hepatocellular carcinoma (HCC) from northern China.

BACKGROUND Metallothionein (MT), acting as an antioxidant and zinc binding protein, may play an important role in regulation of apoptosis. Its differential expression has been documented in various human tumours. MATERIALS AND METHODS MT expression by immunohistochemical staining with a polyclonal antibody and apoptotic cells (APC) by TUNEL technique were investigated in 20 cases of hepatocellular carcinoma (HCC) and 2 normal livers from Northern China. Adjacent normal liver was available from 9 of these cases and 6 had adjacent cirrhotic tissue. There was no difference for MT staining and incidence of APC between normal liver and adjacent normal liver, and thus both were used as control liver. RESULTS Control liver had consistent MT staining with very low incidence of APC. Adjacent cirrhotic liver showed the same intensity of MT staining, with a similar incidence of APC to control liver. Twelve of 20 HCC cases (60%) showed no MT staining, and the rest also showed a low grade of MT staining as compared with control or adjacent cirrhotic livers. The incidence of APC in HCC was markedly higher than that in control liver or adjacent cirrhotic liver. The negative correlation of numbers of APC with MT expression was statistically significant (p < 0.005). The high incidence of APC in liver with a low MT expression was confirmed in double staining for MT and APC. CONCLUSIONS The present investigation from Northern Chinese samples has shown that MT expression in HCC was different from that in other human tumours, such as breast carcinoma. This suggests a different pattern of expression of MT protein in these two kinds of cancer. This investigation is important in understanding the mechanisms of the drug resistance of tumour cells, and may help to design better treatment strategies.
Investigating the reliability of contemporary Chinese pulse diagnosis as a diagnostic tool in Oriental medicine

There have been few studies that evaluate the reliability of the clinical use of pulse diagnosis despite it being a fundamental part of Oriental medicine diagnostics. The objective of this study was to determine the levels of intra-rater and inter-rater reliability of practitioners using an operationally defined method, Contemporary Chinese Pulse Diagnosis (CCPD), to evaluate the radial pulse of volunteer subjects. The study utilised a real-life design to investigate CCPD in a clinical setting. Fifteen volunteer subjects and six testers skilled in the CCPD method were recruited. Two episodes of data collection were conducted 28 days apart as a practical test and retest. For each subject, 30 pulse categories defined by the CCPD system were assessed and reassessed by the same four testers during both phases of testing. All assessments were conducted according to the CCPD method. Intra-rater reliability was measured by comparing individual tester results on day one with day two, while inter-rater agreement and reliability were determined by comparing all testers across both days. The data were analysed using Cohen's kappa coefficient. Kappa values were interpreted according to recommendations from previous clinical studies and parameters considered acceptable when using a tool such as CCPD to assist in clinical diagnosis. Results for intra-rater reliability showed excellent agreement in 43.2%, moderate to good agreement in 42.5% and poor agreement in 14.3% of the raw kappa calculations. Inter-rater agreement demonstrated excellent agreement in 23.5%, moderate to good agreement in 46% and poor agreement in 30.5% of the raw kappa calculations. In conclusion, when the system of pulse diagnosis is operationally defined, acceptable levels of reliability can be achieved. Disagreement was either intrinsic to the subject or indicative of ambiguity within the CCPD system. Accordingly, review of the terminology of the appropriate pulse categories and their clinical reliability is recommended.
Significant Reduction in Delayed Diagnosis of Injury With Implementation of a Pediatric Trauma Service

Background: The occurrence of delayed diagnosis of injury (DDI) among pediatric trauma patients represents a breakdown in trauma care. Although some DDI may be unavoidable, the rate of DDI may be used as a measure of quality improvement. Objective: We sought to investigate DDI in admitted pediatric trauma patients while a designated pediatric trauma response team was used and compare this with the prior incidence of DDI (4.3%) before initiation of the response team. Methods: Primary Children's Medical Center (PCMC) is a regional tertiary pediatric trauma center. This analysis used the prospectively gathered PCMC Trauma Database, and included all hospitalized pediatric trauma patients from 1997 through 2000. Results: A total of 3265 patients were included; no patients were excluded. A DDI occurred in 15 (0.46%; 95% CI: 0.31, 0.79) trauma patients. The DDI patients were more severely injured with significantly higher Injury Severity Scores, lower TRISS Probability of Survival values, longer hospitalizations (P ≤ 0.05, Mann-Whitney U), and were more frequently admitted to the PICU (P ≤ 0.05, χ2) than the non-DDI patient population. In a previous study, our incidence of missed injury was 4.3% (50/1175; 95% CI: 3.3, 5.6); with implementation of a designated trauma response team and trauma service, the incidence of DDI was reduced nearly 10-fold to 0.46% (15/3265; 95% CI: 0.31, 0.79). Conclusions: Implementation of an effective trauma team and trauma service was associated with a significant reduction in DDI.