Miracle-dz/UniFAR-FTUs huggingface dataset:
Deactivating Germline Mutations in LEMD3 Cause Osteopoikilosis and Buschke‐Ollendorff Syndrome, but Not Sporadic Melorheostosis

Autosomal dominant OPK and BOS feature widespread foci of osteosclerotic trabeculae without or with skin lesions, respectively. Occasionally, a larger area of dense bone in OPK or BOS resembles MEL, a sporadic sclerosing disorder primarily involving cortical bone. Others, finding deactivating germline LEMD3 mutations in OPK or BOS, concluded such defects explain all three conditions. We found germline LEMD3 mutations in OPK and BOS but not in sporadic MEL.
Control of Dimorphism in Mucor by Hexoses: Inhibition of Hyphal Morphogenesis

In anaerobic cultures of Mucor rouxii, morphogenesis was strongly dependent on hexose concentration as well as pCO2. At low levels of hexose or CO2, or both, hyphal development occurred; at high levels, the fungus developed as yeast cells. Other dimorphic strains of Mucor responded similarly to hexose and CO2 but differred in their relative sensitivity to these agents. Glucose was the most effective hexose in eliciting yeast development of M. rouxii; fructose and mannose were next; and galactose was last. The fungus may be grown into shapes covering its entire dimorphic spectrum simply by manipulating the hexose concentration of the medium. Thus, at 0.01% glucose, hyphae were exceedingly long and narrow; at higher sugar concentrations, the hyphae became progressively shorter and wider; finally, at about 8% glucose, almost all cells and their progeny were isodiametric (spherical budding cells). Such yeast development occurred without a manifested requirement for exogenous CO2. The stimulation of yeast development by hexose is not an artifact due to increased production of metabolic CO2 (hyphae or yeast cells released metabolic CO2 at similar rates). Presumably, the effect was caused by some other hexose catabolite which interfered with hyphal morphogenesis (apical growth); deprived of its polarity, the fungus grew into spherical yeastlike shapes. Although 10% glucose inhibited the development of hyphae from germinating spores, it did not prevent the elongation of preformed hyphae. This suggests that hexose inhibits hyphal morphogenesis not by blocking the operation of the enzyme complex responsible for apical growth but by preventing its initiation; such inhibition may be regarded as a repression of hyphal morphogenesis.
Recurrent ATM mutations in T-PLL on diverse haplotypes: no support for their germline origin.

The ATM gene has been found to be mutated or deleted in the majority of cases of T cell prolymphocytic leukemia (T-PLL),[1-5][1] and missense mutations were shown to cluster in the highly conserved gene region encoding the ATM kinase domain. [1][1] Recently, Vanasse et al reported that as many as
Effects of atmospheric pollution on a Lichenophagous lepidopteran.

Terrestrial epiphytic algae were used to absorb atmospheric pollutants and this material was then fed to larvae of a bagmoth to assess the toxicological effects of the pollutants. Samples of algae were amended with pesticides to simulate agricultural spray drift and with vehicle exhaust gases to simulate road traffic emissions. Larval mortality, immobilization, and feeding were used as the toxicological endpoints. Feeding was the most sensitive of these, but clear dose-response relationships were observed with all three endpoints. The effects of atmospheric pollution on an impacted environment were then investigated using these organisms. Algal samples were collected along a transect that included an area of arable farming, a motorway, and a woodland. Feeding was reduced when the larvae were fed algae from the areas proximal to the arable land and to the motorway. It is suggested that pesticide spray drift and vehicle exhaust emissions may have been the causal agents for these effects.
Distribution and Functionality of Copy Number Variation across European Cattle Populations

Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.
Relationship between Mycobacterium tuberculosis phylogenetic lineage and clinical site of tuberculosis.

BACKGROUND Genotyping of Mycobacterium tuberculosis has revealed 4 major phylogenetic lineages with differential distribution worldwide. It is not clear whether different lineages are associated with different sites of infection (eg, pulmonary tuberculosis versus extrapulmonary tuberculosis). We sought to determine whether M. tuberculosis lineage is associated with the site of tuberculosis disease. METHODS We conducted a cross-sectional analysis of all culture-confirmed cases of tuberculosis with routinely determined M. tuberculosis spoligotype-defined lineage reported to the US National Tuberculosis Surveillance System from 2004 through 2008. Odds ratios (ORs) were used to assess the relation between disease site and M. tuberculosis lineage, after adjustment for age, sex, human immunodeficiency virus infection status, region of birth, and race/ethnicity. RESULTS Of 53972 reported culture-positive tuberculosis cases, 32000 (59.3%) were cases of M. tuberculosis that included complete spoligotype-based data on lineage. Of these, 23844 (74.5%) were exclusively pulmonary, 5085 (15.9%) were exclusively extrapulmonary, and 3071 (9.6%) were combined pulmonary and extrapulmonary. The percentages of tuberculosis cases that were exclusively extrapulmonary differed by lineage: East Asian, 13.0%; Euro-American, 13.8%; Indo-Oceanic, 22.6%; and East-African Indian, 34.3%. Compared with East Asian lineage, the odds of exclusively extrapulmonary tuberculosis relative to exclusively pulmonary tuberculosis were greater for Euro-American (adjusted OR, 1.3; 95% confidence interval [CI], 1.1-1.4), Indo-Oceanic (adjusted OR, 1.7; 95% CI, 1.5-1.9), and East-African Indian (adjusted OR, 1.6; 95% CI, 1.4-1.9) lineages. CONCLUSIONS Phylogenetic lineage of M. tuberculosis is associated with the site of tuberculosis disease.
Abnormal TDP‐43 expression is identified in the neocortex in cases of dementia pugilistica, but is mainly confined to the limbic system when identified in high and moderate stages of Alzheimer's disease

The transactive response (TAR) DNA binding protein TDP‐43 has been discovered to be a major ubiquitinated protein in frontotemporal lobar degeneration with ubiquitinated tau‐negative inclusions (FTLD‐U), which consequently has been renamed FTLD‐TDP. However, TDP‐43 has since been detected in conditions such as Alzheimer's disease (AD) and dementia with Lewy bodies (DLB) but is often confined to the limbic region rather than the more widespread pattern seen in FTLD‐TDP. Previous work has suggested some relationship between hippocampal sclerosis and TDP‐43 expression. A number of AD cases of both moderate and high stage were examined to determine whether the pattern of TDP‐43 immunohistochemical expression differed and whether any relationship to hippocampal sclerosis could be detected. Cases of hippocampal sclerosis from surgical epilepsy specimens were examined to determine whether hippocampal sclerosis alone could cause abnormal TDP‐43 expression. To establish whether abnormal TDP‐43 expression in other neurodegenerative diseases resembled the pattern and distribution in FTLD‐TDP we examined multiple blocks from a variety of neurodegenerative conditions. In 75% of cases of high‐stage AD there was abnormal TDP‐43 positivity compared to 57% of moderate‐stage AD. While the abnormal TDP‐43 positivity was confined to the limbic regions in the moderate stages, occasional cases in the high stages showed neocortical positivity. Also amygdala and/or entorhinal positivity appeared to precede positivity in the dentate gyrus. No relationship could be established between abnormal TDP‐43 expression and degree of hippocampal sclerosis either in the surgical or autopsy cases. The pattern of distribution of TDP‐43 inclusions from cases of dementia pugilistica most closely resembled that in FTLD‐TDP. This raises the question as to whether there may be some shared pathogenic mechanisms between the two conditions.
HIV‐1 expression protects macrophages and microglia from apoptotic death

Macrophages and microglia are the predominant cells infected with HIV‐1 in the brain, yet the effects of productive HIV infection on the fate of these cells are poorly understood. In this study, we tested the hypothesis that HIV‐1 expression influences cell death in infected macrophages and microglial cells. We detected apoptosis by terminal deoxynucleotidyl transferase‐mediated dUTP nick end labelling (TUNEL) in the cerebral white matter of control and HIV encephalitis (HIVE) brains, and quantitatively analysed apoptotic cells with respect to their location (vessel‐associated vs. parenchymal), CD68 expression, and HIV‐1 p24 expression. There were more vessel‐associated, but not more parenchymal, TUNEL+ cells in HIVE cases as compared to controls. Vessel‐associated TUNEL+ cells were primarily endothelial cells (von Willebrand factor+) or macrophages (CD68+). TUNEL+/CD68+ cells were present in both control and HIVE cases in similar frequencies (2.1 ± 0.7% vs. 1.9 ± 0.7% of total CD68+ populations, respectively). In HIVE, TUNEL+/p24+ cells were 0.4 ± 0.2% of the total p24+ cell population, which was lower than the frequency of TUNEL+/CD68+ cells (1.9 ± 0.7%) in the total CD68+ macrophage population. These results suggest that HIV‐1‐infected macrophages and microglia are resistant to apoptosis, and may contribute to the formation of a central nervous system viral reservoir.
Logical Versus Analogical or Symbolic Versus Connectionist or Neat Versus Scruffy

Engineering and scientific education condition us to expect everything, including intelligence, to have a simple, compact explanation. Accordingly, when people new to AI ask "What's AI all about," they seem to expect an answer that defines AI in terms of a few basic mathematical laws. Today, some researchers who seek a simple, compact explanation hope that systems modeled on neural nets or some other connectionist idea will quickly overtake more traditional systems based on symbol manipulation. Others believe that symbol manipulation, with a history that goes back millennia, remains the only viable approach. Marvin Minsky subscribes to neither of these extremist views. Instead, he argues that AI must use many approaches. AI is not like circuit theory and electromagnetism. There is nothing wonderfully unifying like Kirchhoff's laws are to circuit theory or Maxwell's equations are to electromagnetism. Instead of looking for a "right way," the time has come to build systems out of diverse components, some connectionist and some symbolic, each with its own diverse justification. " - Patrick Winston
Prediction of percent Gleason grade 4/5 by multiple core biopsies

Objective. To evaluate whether percent Gleason grade 4/5 (i.e. the proportion of a tumor occupied by high-grade cancer) can be predicted by multiple needle biopsies. Material and methods. In 115 men, 8–14 (mean 10) biopsies were taken, including eight from standardized positions (apex, mid-medial, mid-lateral and base). Biopsies were reviewed and cancer lengths measured. All men underwent radical prostatectomy. The prostatectomy specimens were totally embedded and tumor volume measured planimetrically. Gleason scores and percent Gleason grade 4/5 were assessed for both biopsy and prostatectomy specimens. Results. Percent Gleason grade 4/5 in prostatectomy specimens was predicted correctly in 34% of cases and within 10%, 20% and 30% in 55%, 64% and 73% of cases, respectively. Biopsies had a sensitivity, specificity and accuracy for Gleason grade 4/5 of 62%, 87% and 69%, respectively. Positive and negative predictive values were 93% and 45%, respectively. The weighted kappa value for agreement was slightly higher for Gleason score (0.685) than for percent Gleason grade 4/5 (0.573). The univariate correlation for percent Gleason grade 4/5 in biopsies and the main tumor was r=0.62, r2=0.39 (p<0.001). In univariate logistic regression, percent Gleason grade 4/5 on biopsies predicted the presence of any Gleason grade 4/5 cancer in the main tumor (p=0.009). Conclusions. Gleason grade 4/5 in prostatectomy specimens correlates with findings in preoperative biopsies. Whether this measure will be used in routine practice remains to be seen.
A Review of Algorithms for Compliant Control of Stiff and Fixed-Compliance Robots

This survey presents the state of the art of basic compliant control algorithms in a unified view of past and present literature. Compliant control is fundamental when dealing with unstructured environments, as in the case of human-robot interaction. This is because it implicitly controls the energy transfer to the environment, providing a safe interaction. In this review, we analyze solutions from traditional robotics, usually involving stiff joints, and recent literature to find common control concepts and differences. To this aim, we bring back every schemas and relative mathematics formulation to a common and simplified scenario. Then, for each schema, we explain its intuitive meaning and report issues raised in the literature. We also propose an expansion of taxonomy to account for recent research.
Characterization of the Staphylococcus aureus strains associated with food 1 poisoning in Shenzhen , China 2 Running Title : Staphylococcus food poisoning in Shenzhen 3

Characterization of the Staphylococcus aureus strains associated with food 1 poisoning in Shenzhen, China 2 Running Title: Staphylococcus food poisoning in Shenzhen 3 Xiaomei Yan, Bing Wang, Xiaoxia Tao, Qinghua Hu, Zhigang Cui, Jianzhong 4 Zhang, Yiman Lin, Yuanhai, You, Xiaolu Shi, Hajo Grundmann 5 National Institute for Communicable Disease Control and Prevention, Chinese 6 Center for Disease Control and Prevention/State Key Laboratory for Infectious 7 Disease Prevention and Control. 155 Changbai Road, Changping District, Beijing, 8 China 102206. 9 Shenzhen Center for Disease Control and Prevention. 8 Longyuan Road, 10 Nanshan District, Shenzhen, Guandong Province, China. 11 University Medical Centre Groningen, Rijksuniversiteit Groningen, The 12 Netherlands/National Institute for Public Health and the Environment (RIVM), 13 Bilthoven, The Netherlands. 14 These authors contributed equally to this work. 15 Corresponding author: zhangjianzhong@icdc.cn 16 17 Copyright © 2012, American Society for Microbiology. All Rights Reserved. Appl. Environ. Microbiol. doi:10.1128/AEM.01165-12 AEM Accepts, published online ahead of print on 13 July 2012
The Macro-Regional Scale of Silver Production in Iberia During the First Millennium BC in the Context of Mediterranean Contacts

The extraction of silver has traditionally been considered as one of the main incentives for the Phoenician expansion throughout the Mediterranean and their settlement in Iberia. In this paper, we approach the organization of silver production in Iberia during the Early Iron Age through the study of the evidence of production currently available and the development of Lead Isotope Analysis (LIA). Previous results (Hunt 2003; Stos Gale 2001; Kassianidou 1992) are considered in the light of new data. The extraction of silver from complex minerals noticeably intensifies in south-west Iberia. Imports of exogenous lead, needed for the extraction of silver from these complex minerals, are evident. Supplies of lead come in from other regions of Iberia, such as Gador, Cartagena/Mazarron, Linares or even the mining district of Molar-Belmunt-Falset (MBF) in Catalonia. This picture reveals that the organization of silver production was much more complex than initially thought, with the articulation of an exchange network of raw materials at a macro-territorial scale embracing almost all Iberia. The socioeconomic implications that control of these networks of lead distribution could have had are also discussed.
Genetic Polymorphisms of Hepatic ABC-Transporter in Patients with Hepatocellular Carcinoma

We examined whether genetic polymorphisms of efflux transporters in hepatocytes are associated with susceptibility to develop hepatocellular carcinoma (HCC). Genetic polymorphisms of drug transporters expressed in hepatocytes were analyzed using DNA samples from hepatitis C virus (HCV)-seropositive cirrhotic patients with HCC (n = 58), and allele and haplotype frequencies were compared with those in healthy subjects (n = 61). To search for single nucleotide polymorphisms (SNPs) in HCC susceptibility genes, 34 SNPs in 6 efflux transporters [MDR1 (ABCB1), ABCC1, ABCC2, ABCC3, ABCG2 and ABCB11] were determined. No significant association was observed for any single SNP; however, some haplotypes in ABCC1 and ABCB11 were associated with HCC. Furthermore, three combinations of SNPs (3435C > T in ABCB1 and 825T > C in ABCC1), (3435C > T in ABCB1 and -15281_-15278CTCT > delete in ABCB11), and (825T > C in ABCC1 and -15281_-15278CTCT > delete in ABCB11) were significantly associated with HCC. The present study suggests that genetic variations of ABC transporters such as ABCB1, ABCB11, and ABCC1 are associated with susceptibility to develop HCC, implying that aberrant hepatic clearance of toxic substances may increase the risk of hepatocarcinogenesis. Further studies of how these polymor-phisms are associated with phenotypic differences are warranted.
Aiming higher to enhance professionalism: beyond accreditation and certification.

Professions have special privileges in the United States. There are intangible benefits such as prestige, but more importantly, professions have the dearly prized privilege of autonomy. With this privilege comes the expectation that a profession will establish codes of conduct and promote high standards of quality among its members. From the standpoint of creating codes of conduct, the medical profession has been a role model. In 1847, the newly formed American Medical Association met in Philadelphia, Pennsylvania, as the first national professional medical organization in the world. At that meeting, its members adopted the world's first national code of professional medical ethics and established standards for education, training, and conduct.1 More recently, the American Board of Internal Medicine, the American College of Physicians Foundation, and the European Federation of Internal Medicine jointly authored Medical Professionalism in the New Millennium: A Physician Charter.2 The charter established a set of professional responsibilities that inform physicians about how they should practice: to follow the fundamental
Identifying early decline of physical function in community-dwelling older women: performance-based and self-report measures.

BACKGROUND AND PURPOSE The ability to identify early decline in physical function is important, but older people experiencing decline may fail to report the early changes in physical function. The purpose of this study was to compare the descriptions of physical function in community-dwelling older women obtained using performance-based and self-report measures. SUBJECTS AND METHODS One hundred seventy community-dwelling women with a mean age of 74.3 years (SD=4.3, range=56.6-83.6) completed the activities of daily living (ADL), instrumental activities of daily living (IADL) and social activity (SA) sections of the Functional Status Questionnaire (FSQ). They also completed performance-based measures of gait speed and the 7-item Physical Performance Test (PPT). RESULTS The majority of the women scored at the ceiling for the self-report measures of function (ADL=77%, IADL=61%, SA=94%), whereas only 7% scored at the ceiling for the PPT and 30% scored at the ceiling for gait speed (defined as >1.2 m/s). For 2 items of the FSQ, sensitivity was low (8% and 9%) and specificity was high (97% and 98%) compared with performance on the PPT. DISCUSSION AND CONCLUSION In this sample of community-dwelling older women, performance-based measures identified more limitations in physical function than did self-report measures.
The WRKY 57 Transcription Factor Affects the Expression of Jasmonate ZIM-Domain Genes Transcriptionally to Compromise Botrytis cinerea Resistance 1

Although necrotrophic pathogens cause many devastating plant diseases, our understanding of the plant defense response to them is limited. Here, we found that loss of function of WRKY57 enhanced the resistance of Arabidopsis (Arabidopsis thaliana) against Botrytis cinerea infection. Further investigation suggested that the negative regulation of WRKY57 against B. cinerea depends on the jasmonic acid (JA) signaling pathway. Chromatin immunoprecipitation experiments revealed that WRKY57 directly binds to the promoters of JASMONATE ZIM-DOMAIN1 (JAZ1) and JAZ5, encoding two important repressors of the JA signaling pathway, and activates their transcription. In vivo and in vitro experiments demonstrated that WRKY57 interacts with nuclear-encoded SIGMA FACTOR BINDING PROTEIN1 (SIB1) and SIB2. Further experiments display that the same domain, the VQ motif, of SIB1 and SIB2 interact with WRKY33 and WRKY57. Moreover, transient transcriptional activity assays confirmed that WRKY57 and WRKY33 competitively regulate JAZ1 and JAZ5, SIB1 and SIB2 further enhance these competitions of WRKY57 to WRKY33. Therefore, coordinated regulation of Arabidopsis against B. cinerea by transcription activators and repressors would benefit plants by allowing fine regulation of defense.
Race/ethnicity, vaginal flora patterns, and pH during pregnancy.

OBJECTIVES To investigate the relationship between bacterial vaginosis during pregnancy and black race/ethnicity. STUDY DESIGN Gram staining was used to evaluate vaginal flora in 842 women at 24 to 29 weeks' gestation. RESULTS Overall, 22.3% of blacks and 8.5% of whites had bacterial vaginosis. Vaginal pH and flora differed significantly by race/ethnicity; blacks were more likely to have pH > or = 4.5, no lactobacilli, small gram-variable and -negative rods, and Mobiluncus compared with whites (odds ratios 1.6, 1.5, 1.4, and 10.6, respectively). Quantity of morphotypes also differed, especially for Mobiluncus. Among women with Mobiluncus present (12.0% of blacks and 1.3% of whites), 73.3% of blacks compared with 40.0% of whites had the highest level. Adjustment for sociodemographics, sexual activity, sexually transmitted diseases, health behavior, and sexual hygiene did not explain these differences. CONCLUSION We observed race/ethnicity differences in vaginal flora ecology. These differences may ultimately play a role in the larger proportion of preterm deliveries among black women compared with white women.