Miracle-dz/UniFAR-FTUs huggingface dataset:
TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data

TP53 gene mutations are one of the most frequent somatic events in cancer. The IARC TP53 Database (http://p53.iarc.fr) is a popular resource that compiles occurrence and phenotype data on TP53 germline and somatic variations linked to human cancer. The deluge of data coming from cancer genomic studies generates new data on TP53 variations and attracts a growing number of database users for the interpretation of TP53 variants. Here, we present the current contents and functionalities of the IARC TP53 Database and perform a systematic analysis of TP53 somatic mutation data extracted from this database and from genomic data repositories. This analysis showed that IARC has more TP53 somatic mutation data than genomic repositories (29,000 vs. 4,000). However, the more complete screening achieved by genomic studies highlighted some overlooked facts about TP53 mutations, such as the presence of a significant number of mutations occurring outside the DNA‐binding domain in specific cancer types. We also provide an update on TP53 inherited variants including the ones that should be considered as neutral frequent variations. We thus provide an update of current knowledge on TP53 variations in human cancer as well as inform users on the efficient use of the IARC TP53 Database.
Parkinson’s disease and driving ability

Objectives: To explore the driving problems associated with Parkinson’s disease (PD) and to ascertain whether any clinical features or tests predict driver safety. Methods: The driving ability of 154 individuals with PD referred to a driving assessment centre was determined by a combination of clinical tests, reaction times on a test rig and an in-car driving test. Results: The majority of cases (104, 66%) were able to continue driving although 46 individuals required an automatic transmission and 10 others needed car modifications. Ability to drive was predicted by the severity of physical disease, age, presence of other associated medical conditions, particularly dementia, duration of disease, brake reaction, time on a test rig and score on a driving test (all p<0.001). The level of drug treatment and the length of driving history were not correlated. Discriminant analysis revealed that the most important features in distinguishing safety to drive were severe physical disease (Hoehn and Yahr stage 3), reaction time, moderate disease associated with another medical condition and high score on car testing. Conclusions: Most individuals with PD are safe to drive, although many benefit from car modifications or from using an automatic transmission. A combination of clinical tests and in-car driving assessment will establish safety to drive, and a number of clinical correlates can be shown to predict the likely outcome and may assist in the decision process. This is the largest series of consecutive patients seen at a driving assessment centre reported to date, and the first to devise a scoring system for on-road driving assessment.
TIRAMISU: A Polyhedral Compiler for Dense and Sparse Deep Learning

In this paper, we demonstrate a compiler that can optimize sparse and recurrent neural networks, both of which are currently outside of the scope of existing neural network compilers (sparse neural networks here stand for networks that can be accelerated with sparse tensor algebra techniques). Our demonstration includes a mapping of sparse and recurrent neural networks to the polyhedral model along with an implementation of our approach in TIRAMISU, our state-of-the-art polyhedral compiler. We evaluate our approach on a set of deep learning benchmarks and compare our results with hand-optimized industrial libraries. Our results show that our approach at least matches Intel MKL-DNN and in some cases outperforms it by 5x (on multicore-CPUs).
A comparison of several calcium antagonists on uterine, vascular and cardiac muscles from the rat

1 An assessment was made of the potencies of nifedipine, gallopamil, diltiazem, cinnarizine and salbutamol as inhibitors of tension development by the uterus and cardiovascular tissues from the term pregnant rat. 2 The rank order of potency was nifedipine > gallopamil > diltiazem for those preparations on which these compounds were potent, viz. spontaneous and oxytocin‐induced tension development of the uterus, spontaneous tension development of hepatic portal vein, potassium chloride (KCl)‐induced pressure rises of perfused mesenteric bed and electrically‐stimulated (0.5 Hz) ventricular muscle. 3 The rank order of potency of nifedipine, gallopamil and diltiazem was different for those preparations on which they exhibited low potency, viz. noradrenaline‐induced pressure rises of perfused mesenteric bed and tension development of aorta. 4 Gallopamil and diltiazem, but not nifedipine, were more potent against tension development by ventricular muscle stimulated at 2.5 Hz than at 0.5 Hz, suggesting that nifedipine interacts at a different site from the other compounds. 5 Cinnarizine was less potent than the other calcium antagonists on the uterus and portal vein, was the second most potent compound against KCl‐induced pressure rises of the mesenteric bed and was equipotent against responses to noradrenaline and KCl of the mesenteric bed (unlike the other compounds). This suggests that the site of action of cinnarizine differs from that of the other calcium antagonists. 6 Nifedipine, gallopamil and diltiazem, like salbutamol, exhibited selectivity for inhibition of tension development by the uterus relative to the cardiovascular tissues.
Partial discharge, dissipation factor, and corona aspects for high voltage electric generator stator bars and windings

High voltage stator windings in modern electric generators are subject to high electrical, mechanical, and thermal stress. Operation of these machines in both air and high pressure hydrogen results in different considerations. Operation in the air environment does not offer the dielectric advantages of operating in high-pressure hydrogen. The two major design factors that are significant for the design of high voltage stator bars to be operated in air, are corona activity and PD activity. These of course are closely related. With the movement to increasing the power density of generators, which means operation at higher voltages and higher insulation stress levels, it has become more critical to be sure the design constraints are met in the stator bar design to minimize both partial discharge activity and corona activity involving the stator bars. The stator bar insulation system must be designed for minimum partial discharge activity and ideally is corona free at the stator winding operating stress levels, and at the operating conditions (temperature and pressure) the generator is subject to. This paper will present the findings associated with the development work in designing, testing and implementing a PD reduced and corona free design.
Efficacy of a telephone‐based medical nutrition program on blood lipid and lipoprotein metabolism: Results of Our Healthy Heart

AIM Derangements in blood lipid and lipoprotein metabolism are one of the leading causes of coronary heart disease (CHD). Therapeutic lifestyle changes such as diet and exercise are often prescribed to improve blood lipid and lipoprotein characteristics, but the efficacy of a telephone-based health coaching program has not been thoroughly explored. Our purpose was to examine effects of the Our Healthy Heart (OHH) Program on blood lipid and lipoprotein characteristics of individuals with mixed dyslipidaemia. METHODS Cholesterol content of serum very low-density lipoprotein (VLDL), low-density lipoprotein (LDL) and high-density (HDL) subfractions and apolipoprotein concentrations were measured by vertical-density ultracentrifugation (Vertical Auto Profile (VAP)) from 1522 individuals with mixed dyslipidaemia (age 18-99 years, body mass index (BMI) 25-40, 62.7% female). Telephone-based health coaching (OHH, n = 722) or standard care (Control, n = 800) was provided for six months followed by VAP to evaluate changes in lipid and lipoprotein concentrations. Controls were obtained from individuals with similar blood lipid/lipoprotein characteristics who did not participate in the OHH Program. Coaches collected baseline self-reported data on anthropometrics, food intake and exercise. Participants in the OHH group were then prescribed a hypocaloric 500 kcal/day caloric deficit with encouragement to participate in physical activity. A two-way ANOVA was used to examine differences between groups over time, with results presented as means ± standard deviation. RESULTS Health coaching significantly decreased serum concentrations of apoB100 (104.5 ± 25.8-94.3 ± 24.8 mg/dL), shifted LDL pattern size from B to A or A/B in over 60% of the OHH group and decreased cholesterol content of all VLDL subfractions (P < 0.05) compared to the control. CONCLUSIONS Telephone-based health coaching recommendations to reduce dietary energy intake and increase physical activity produced significant improvements in cholesterol content of atherogenic lipoproteins, which are known to increase CHD risk.
Compromised Diet Quality is Associated with Decreased Renal Function in Children with Chronic Kidney Disease

Nutritional status of children with chronic kidney disease (CKD) is important since it affects growth and development. This study was to investigate overall diet quality measured by nutrient intake adequacy, nutrient density, and several dietary habits in children with CKD and its relationship with clinical parameters according to glomerular filtration rate (GFR). Assessment of nutritional status and diet quality was conducted in nineteen children with CKD. Average Z-scores of height, weight and body mass index (BMI) in the participants were less than standard growth rate. Nutritional status, such as Z-scores of height (p < 0.05) and serum total protein (p < 0.05), were significantly lower in the children with GFR < 75 mL/min/1.73 m2 compared to those with GFR ≥ 75 mL/min/1.73 m2. Nutrition adequacy ratio of energy, thiamin, riboflavin, vitamin B6, folate, iron, and zinc and overall diet quality were significantly poorer in the children with GFR < 75 mL/min/1.73 m2. Poorer appetite and avoidance of food were observed in the children with higher blood urea nitrogen (BUN). Intakes of iron, zinc, thiamin, niacin, and vitamin B6 were positively correlated with GFR. Intakes of calcium, potassium and folate were positively correlated with BUN, while protein intakes were negatively correlated. Overall nutrient intakes were inadequate and diet quality was decreased as kidney function was decreased. Dietary habit and appetite were also related with kidney function in this study subjects. Systemic efforts of nutritional intervention are imperative to prevent deteriorating growth and development and improve the nutritional status in children with CKD.
On tune deafness (dysmelodia): frequency, development, genetics and musical background

143th the aid of the Distorted Tunes Test a group of British adults could be established whose melodic aptitude was below a certain level and whom we called tune deaf. They are only a fraction of those popularly called tone deaf. The Distorted Tunes Test is only slightly correlated with pitch discrimination, short term tonal memory or number memory. In children ability to pass the Distorted Tunes Test develops at greatly varying speeds and to a varying degree, reaching stability in adolescence. Tune deafness has a familial distribution and segregates in away suggesting an autosomsl dominant brait with imperfect penetrance. Some degree of positive assortatire mating has been established.
Analysis of a DC XY-actuator

The proposed XY-actuator is composed of a ferromagnetic core, a set of two perpendicular planar windings, and a mover fitted with permanent magnets that produce the excitation magnetic field. The actuator was studied under the use of two different armature cores: solid steel, and a soft magnetic composite (SMC). The movement of the mover over the working plan occurs when the coils of the windings are excited. Owing to the velocity, eddy currents are induced in the core accordingly. As a result, a damping effect occurs. It can be limited with the use of a material with high electrical resistivity such as the SMC. A numerical dynamic analysis by a finite element model produced the verification of current induced, as well as the magnetic flux density distribution, and the forces involved. With the experimental results, it was possible to obtain an electromagnetic coefficient of friction due the eddy currents.
Karyotypic abnormalities and clinical aspects of patients with multiple myeloma and related paraproteinemic disorders

Karyotypic abnormalities were detected in the malignant cells of 6 of 18 patients with multiple myeloma (MM). Six patients with benign monoclonal gammopathy, one with amyloidosis of immunoglobulin origin, and two with Waldenström's macroglobulinemia had normal karyotypes. All six MM patients with aneuploidy were in a group of 10 patients in an accelerated or relapse phase of their disease and four had high serum paraprotein levels (7.92, 6.24, 6.80, and 4.24 g/dl, respectively) when their abnormal karyotypes were detected. Five of the 6 MM patients with aneuploidy had received prior chemotherapy. Aneuploidy was not observed in 8 stable MM patients. Abnormalities of chromosome 14 were present in all 6 patients, with a 14q+ marker in 5 and loss of No. 14 in 1. A translocation between Nos. 11 and 14 was found in aneuploid cells of 2 patients who had plasma cell leukemia (PCL). However, the break point in the long arm of No. 11 differed in the 2 patients. A gain of Nos. 5, 9, and 11 was seen in 3 patients, a gain of No. 1 in 2, and rearrangements of No. 1 in 5 MM patients, including all 4 who had a 14q+ marker chromosome initially. A deletion of chromosome 6 at band q25 was detected in 2 MM patients and a pericentric inversion of No. 6 (6p21 to 6q13) was seen in the patient with PCL. Three of 4 MM patients had a nonrandom loss of one chromosome 8. Two other MM patients, who were treated with melphalan and prednisone, developed acute nonlymphocytic leukemia (ANLL) 2+ and 4+ years after the diagnosis of MM. Marrow cells of one patient showed a 5q‐ chromosome and a constitutional translocation involving Nos. 13 and 14 during the preleukemic stage; during the leukemic phase, the karyotype evolved to 50 chromosomes including extra chromosomes 1, 6, 8, 10, and 21 and a missing 7, in addition to the originally detected 5q‐ and the 13/14 translocation. The peripheral blood from the other patient was hypodiploid, with a missing chromosome 7 and a translocation between 3q and 9p. These patterns of chromosome change resemble those of ANLL rather than MM and are similar to the changes seen in ANLL after treated malignant lymphoma. Cancer 44:630‐644, 1979.
Large juxtamedullary glomeruli and afferent arterioles in healthy primates.

BACKGROUND Differences in the functional demands of superficial and juxtaglomerular nephrons could result in differences in glomerular size between these two types of nephrons. This concept is based on animal models in which the juxtamedullary glomeruli and afferent arteriole diameters are indeed larger than those in the outer cortical zones. However, this difference was not confirmed in human necropsy studies. To obtain further information in living primates, we have made unbiased estimates of glomerular and afferent arteriole dimensions in three cortical zones (superficial, midcortical, and juxtamedullary) in young, adult, normotensive monkeys. METHODS In each animal (N = 6), the right kidney was perfusion fixed and prepared for unbiased stereological estimation of glomerular number and size. The left kidney vasculature was fixed while relaxed and at a known intravascular pressure. Thereafter, afferent arteriolar dimensions were estimated using light and confocal microscopy. RESULTS The mean glomerular volume was variable between animals (coefficient of variation, 23%) and was largest in the juxtamedullary zone. Afferent arteriolar lumen diameter varied little between animals (coefficient of variation, 3%), but was also the largest in the juxtamedullary zone. No sclerotic glomeruli were found in any of the animals. CONCLUSION The findings show that in normal primates, as previously shown in other animals, juxtamedullary glomeruli and afferent arteriolar diameters are larger compared with those in the outer cortical zones.
Ge overlayer and surface alloy structures on Pt(100) studied using alkali ion scattering spectroscopy, x-ray photoelectron spectroscopy and x-ray photoelectron diffraction

We have investigated surface structures formed by deposition of Ge on a Pt(100) substrate by using a multi-technique approach utilizing alkali ion scattering spectroscopy (ALISS), x-ray photoelectron spectroscopy (XPS), and x-ray photoelectron diffraction (XPD). ALISS was used to distinguish Ge overlayers from incorporated alloy layers for the surface structures reported, and to supply structural information about the surface alloy or ‘layer compound’ formed by the deposition of 1.5-ML Ge. A Ge adlayer forms following the deposition of 0.2-ML Ge on Pt(100) and annealing at 600 K. ALISS revealed that Ge adatoms in these overlayers had 1D (incomplete c(2 × 2)) Ge–Ge ordering along [010] and equivalent directions, even though this was not directly apparent in observations using LEED and STM. A c(2 × 2)-Ge overlayer was produced after 0.5 ML-Ge deposition on Pt(100) and annealing at 600 K. Deposition of 1.5-ML Ge on Pt(100) and annealing at 600 K caused extensive Ge interdiffusion into the third (subsurface) layer, while the first and second layers remained as a c(2 × 2) Ge overlayer and (1 × 1) Pt layer, respectively. We propose that the Pt(100) substrate thus is ‘capped’ by an alloy film with the structure of a body-centered tetragonal Pt2Ge layer compound, which is terminated by a pure-Ge layer that is indistinguishable from a c(2 × 2)-Ge adlayer. This explains the apparently ‘strange’ result that even though extensive Ge interdiffusion was occurring deeply into the Pt bulk during annealing at 900 and 1200 K, a Ge overlayer remained on the surface. XPS spectra showed a +0.5 eV binding energy shift of the Ge 3d core level and a small (0–0.1 eV) positive shift of the Pt 5d core level compared to Ge(100) and Pt(100) surfaces for the c(2 × 2)-Ge overlayer. There was no effect on these binding energies upon formation of the Pt2Ge layer compound at the surface, and this indicates similar Ge–Pt interactions in the two cases. Compared to other overlayers of Group-IV atoms on metal surfaces, the Ge overlayer on Pt(100) was extraordinarily stable.
Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus

CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, and III) each target destruction of foreign nucleic acids via structurally and functionally diverse effector complexes (crRNPs). CRISPR-Cas effector complexes are comprised of CRISPR RNAs (crRNAs) that contain sequences homologous to the invading nucleic acids and Cas proteins specific to each immune system type. We have previously characterized a crRNP in Pyrococcus furiosus (Pfu) that contains Cmr (Type III-B) Cas proteins associated with one of two size classes of crRNAs and cleaves complementary target RNAs. Here, we have isolated and characterized two additional native Pfu crRNPs containing either Csa (Type I-A) or Cst (Type I-G) Cas proteins and distinct profiles of associated crRNAs. For each complex, the Cas proteins were identified by mass spectrometry and immunoblotting and the crRNAs by RNA sequencing and Northern blot analysis. The crRNAs associated with both the Csa and Cst complexes originate from all seven Pfu CRISPR loci and contain identical 5′ ends (8-nt repeat-derived 5′ tag sequences) but heterogeneous 3′ ends (containing variable amounts of downstream repeat sequences). These crRNA forms are distinct from Cmr-associated crRNAs, indicating different 3′ end processing pathways following primary cleavage of common pre-crRNAs. Like other previously characterized Type I CRISPR-Cas effector complexes, we predict that the newly identified Pfu Csa and Cst crRNPs each function to target invading DNA, adding an additional layer of protection beyond that afforded by the previously characterized RNA targeting Cmr complex.
Genome‐wide scan in 124 Indonesian sib‐pair families with schizophrenia reveals genome‐wide significant linkage to a locus on chromosome 3p26‐21

Variation in incidence of schizophrenia between populations with different ethnical background may reflect population specific differences in nature and composition of genetic and environmental factors. In order to investigate whether there are population specific susceptibility genes for schizophrenia, we collected in Indonesia families with two or more affected siblings and, as far as available, parents and unaffected siblings, suitable for genetic linkage‐ and association studies. After checking extensively for incompatibilities with Mendelian inheritance as well as for errors in sampling, we used 124 families from the sample of 152 originally ascertained families for linkage analysis. Genotyping was performed at the NHLBI Mammalian Genotyping Service at Marshfield Research Organisation using the Screening Set 16, which comprises 402 Short Tandem Repeat Polymorphisms (STRPs). The genotypes of 540 individuals including 267 affected with schizophrenia were used for analysis. Multipoint sib‐pair linkage analysis was carried out by estimation of—allele sharing derived—maximum likelihood LOD scores (MLS) in 154 sib‐pair combinations. We obtained a genome‐wide significant MLS of 3.76 on chromosome 3p26.2‐25.3. Genome‐wide significance was estimated by performing 10,000 simulated genomescans. Additional loci were detected on 1p12, which produced suggestive evidence for linkage (MLS = 2.35), as well as on 5q14.1 (MLS = 1.56), 5q33.3 (MLS = 1.11), and 10q (MLS = 1.17), where linkage had been reported previously. In conclusion, our study detected a region with genome‐wide significant linkage, which will serve as starting point for identification of schizophrenia susceptibility genes in the Indonesian population. © 2008 Wiley‐Liss, Inc.
Recognition Without Words: Using Taste to Explore Survival Processing.

Many educational demonstrations of memory and recall employ word lists and number strings; items that lend themselves to semantic organization and "chunking. " By applying taste recall to the adaptive memory paradigm, which evaluates memory from a survival-based evolutionary perspective, we have developed a simple, inexpensive exercise that defies mnemonic strategies. Most adaptive memory studies have evaluated recall of words encountered while imagining survival and non-survival scenarios. Here, we've left the lexical domain and hypothesized that taste memory, as measured by recognition, would be best when acquisition occurs under imagined threat of personal harm, namely poisoning. We tested participants individually while they evaluated eight teas in one of three conditions: in one, they evaluated the toxicity of the tea (survival condition), in a second, they considered the marketability of the tea and, in the third, they evaluated the bitterness of the tea. After a filler task, a surprise recognition task required the participants to taste and identify the eight original teas from a group of 16 that included eight novel teas. The survival condition led to better recognition than the bitterness condition but, surprisingly, it did not yield better recognition than the marketing condition. A second experiment employed a streamlined design more appropriate for classroom settings and failed to support the hypothesis that planning enhanced recognition in survival scenarios. This simple technique has, at least, revealed a robust levels-of-processing effect for taste recognition and invites students to consider the adaptive advantages of all forms of memory.