Miracle-dz/UniFAR-FTUs huggingface dataset:
The functional costs and benefits of dietary restriction in Drosophila

Dietary restriction (DR) extends lifespan in an impressively wide array of species spanning three eukaryotic kingdoms. In sharp contrast, relatively little is known about the effects of DR on functional senescence, with most of the work having been done on mice and rats. Here we used Drosophila melanogaster to test the assumption that lifespan extension through DR slows down age‐related functional deterioration. Adult virgin females were kept on one of three diets, with sucrose and yeast concentrations ranging from 7% to 11% to 16% (w/v). Besides age‐specific survival and fecundity, we measured starvation resistance, oxidative stress resistance, immunity, and cold‐stress resilience at ages 1, 3, 5, and 7 weeks. We confirmed that DR extends lifespan: median lifespans ranged from 38 days (16% diet) to 46 days (11% diet) to 54 days (7% diet). We also confirmed that DR reduces fecundity, although the shortest‐lived flies only had the highest fecundity when males were infrequently available. The most striking result was that DR initially increased starvation resistance, but strongly decreased starvation resistance later in life. Generally, the effects of DR varied across traits and were age dependent. We conclude that DR does not universally slow down functional deterioration in Drosophila. The effects of DR on physiological function might not be as evolutionarily conserved as its effect on lifespan. Given the age‐specific effects of DR on functional state, imposing DR late in life might not provide the same functional benefits as when applied at early ages.
Pronunciation of proper names with a joint n-gram model for bi-directional grapheme-to-phoneme conversion

Pronunciation of proper names is known to be a difficult problem, but one of great practical importance for both speech synthesis and speech recognition. Recently a few data-driven grapheme-to-phoneme conversion techniques have been proposed to tackle this problem. In this paper we apply the joint n-gram model for bi-directional grapheme-to-phoneme conversion, which has already been shown to achieve excellent results on general tasks, to the more specific task of converting between name pronunciations and spellings. The performance of our technique on generating name pronunciations exceeds that of other techniques even when they use additional information. We find the reverse task, of generating orthographic transcriptions from phonemic input, to be a much more difficult task for names than for common words. However, we derive valuable information from our results about the potential of sub-lexical recognition of novel proper names.
Discovery of Novel Functional Variants and Extensive Evaluation of CYP2D6 Genetic Polymorphisms in Koreans

Our objectives were to identify CYP2D6 genetic polymorphisms in a Korean population, to compare the allele frequencies with those of other ethnic groups, and to evaluate variant-induced functional variations in dextromethorphan (DM) metabolism in vitro and in vivo. Thirty-eight single nucleotide polymorphisms of CYP2D6 were identified by direct DNA sequencing in 51 Koreans. An extended set of 707 subjects were screened for the identified variants. A group of 202 healthy subjects was subjected to phenotypic analysis on DM metabolism. CYP2D6*10 was found to be the most frequent allele (45.6%), followed by CYP2D6*1 (32.3%), *2 (9.9%), *5 (5.6%), *41 (2.2%), *49 (1.4%), and some other rare alleles (<1%). The newly identified E418K and S183Stop were assigned as CYP2D6*52 and CYP2D6*60, respectively, by the Human P450 (CYP) Allele Nomenclature Committee. Individuals having the CYP2D6*10/*49 genotype (n = 5) exhibited a significant decrease in CYP2D6 metabolic activity compared with those with the CYP2D6*1/*1 genotype (n = 31) (P < 0.019). Variations in CYP2D6 protein levels in liver tissues (n = 49) were observed with CYP2D6 genotypes, and correlation between the CYP2D6 protein content and the activity was significant (r2 = 0.7). Given the importance of CYP2D6 in drug metabolism, subjects with the CYP2D6*10/*49 genotype may benefit from genotype analysis to achieve optimal drug therapy.
FGF‐2 converts mature oligodendrocytes to a novel phenotype

Fibroblast growth factor (FGF)‐2 differentially regulates oligodendrocyte progenitor proliferation and differentiation in culture, and modulates gene expression of its own receptors, in a developmental and receptor type‐specific manner (Bansal et al., 1996a,b). Three FGF receptors (types 1, 2, 3) are expressed in postmitotic, terminally differentiating oligodendrocytes. Exposure of such cells to FGF‐2 results in: (a) the down‐regulation of myelin‐specific gene expression (e.g., ceramide galactosyltransferase, 2′,3′‐cyclic nucleotide 3′‐phosphohydrolase, myelin basic protein, proteolipid protein), (b) dramatic increases in the length of cellular processes in a time‐ and dose‐dependent manner, (c) re‐entrance into the cell cycle without accompanying mitosis, and (d) the alteration of the expression of both low‐ and high‐affinity FGF receptors. Compared to oligodendrocyte progenitors, the differentiated oligodendrocytes treated with FGF‐2 incorporate BrdU at a slower rates, exhibit different patterns of both FGF high‐ and low‐affinity (syndecans) receptors, and are morphologically very different. In addition, they do not re‐express the progenitor markers A2B5, NG2 or PDGFα receptor. Therefore, although the FGF‐treated cells lose their differentiated OL/myelin markers, they do not revert to progenitors and clearly represent a different, apparently novel, phenotype both morphologically and biochemically, which we have termed NOLs. These data indicate that terminally differentiated oligodendrocytes retain the plasticity to reprogram their differentiation fate under the influence of environmental factors. The possible significance of this response to FGF relative to normal and pathological physiology is discussed. In particular, on the basis of these data we predict the appearance of cells in and around multiple sclerosis plaques with the phenotype O4+, NG2−, A2B5−, O1−, MBP−. J. Neurosci. Res. 50:215–228, 1997. © 1997 Wiley‐Liss, Inc.
Variation in cadaveric organ donor rates in the UK.

BACKGROUND Considerable variation exists in the organ donation rate between kidney retrieval areas (KRAs) within the UK. The causes for this are unknown. This study examines whether or not observed variations are correlated with various possible explanatory factors. METHODS A geographical study involving Poisson regression analysis was carried out of all 21 KRAs in the UK in 1999 and 2000, with donor rate as dependent variable, and the following independent variables: road traffic accident, intracerebral haemorrhage and other trauma death rates; intensive care unit (ICU) bed numbers; co-location of transplant and neurosurgical units; population ethnicity; proportion of the population on the organ donor register; transplant coordinator numbers; and transplant unit numbers. Main outcome measures were: donor rate in each KRA; strength of association between independent and dependent variables; and magnitude of changes in the donor rate associated with changes in independent variables. RESULTS The donor rate varied between eight and 27.4 donors per million population per year. There was an association between donor rate and general ICU bed numbers (more beds associated with a higher donor rate), but this was of borderline statistical significance (P = 0.065). However, the donor rate was negatively associated (P = 0.02) with neurosurgical ICU bed numbers (more beds, fewer donors) and the proportion of the population from minority ethnic communities. There was no statistically significant association with the other independent variables. CONCLUSIONS There is significant variation in the organ donor rate between different parts of the UK. More research is needed to explore the counter-intuitive association between neurosurgical ICU beds and donations, and to determine the remaining causes of the observed variation.
Characterization of Kidney and Skeleton Phenotypes of Mice Double Heterozygous for Foxc1 and Foxc2

Foxc1 and Foxc2 play key roles in mouse development. Foxc1 mutant mice develop duplex kidneys with double ureters, and lack calvarial and sternal bones. Foxc2 null mice have been reported to have glomerular abnormalities in the kidney and axial skeletal anomalies. Expression patterns of Foxc1 and Foxc2 overlap extensively and are believed to have interactive roles. However, cooperative roles of these factors in glomerular and skeletal development are unknown. Therefore, we examined the kidneys and skeleton of mice that were double heterozygous for Foxc1 and Foxc2. Double heterozygotes were generated by mating single heterozygotes for Foxc1 and Foxc2. Newborn double heterozygous mice showed many anomalies in the kidney and urinary tract resembling Foxc1 phenotypes, including duplex kidneys, double ureters, hydronephrosis and mega-ureter. Some mice had hydronephrosis alone. In addition to these macroscopic anomalies, some mice had abnormal glomeruli and disorganized glomerular capillaries observed in Foxc2 phenotypes. Interestingly, these mice also showed glomerular cysts not observed in the single-gene knockout of either Foxc1 or Foxc2 but observed in conditional knockout of Foxc2 in the kidney. Serial section analysis revealed that all cystic glomeruli were connected to proximal tubules, precluding the possibility of atubular glomeruli resulting in cyst formation. Dorsally opened vertebral arches and malformations of sternal bones in the double heterozygotes were phenotypes similar to Foxc1 null mice. Absent or split vertebral bodies in the double heterozygotes were phenotypes similar to Foxc2 null mice, whilst hydrocephalus noted in the Foxc1 phenotype was not observed. Thus, Foxc1 and Foxc2 have a role in kidney and axial skeleton development. These transcription factors might interact in the regulation of the embryogenesis of these organs.
Covered and uncovered self-expandable metallic Hanarostents are equally efficacious in the drainage of extrahepatic malignant strictures. Results of a double-blind randomized study

Abstract Background. Self-expandable metallic stents (SEMS) placement is a standard treatment for inoperable malignant bile duct strictures. Covered SEMS have been introduced to avoid stent occlusion by tumor ingrowth. The aims were to compare covered and uncovered stents in terms of patency, efficacy and complication rate. Material and methods. Consecutive patients with inoperable malignant distal biliary strictures were included in the study and randomized to receive a covered (n = 34) or uncovered (n = 34) Hanaro SEMS. Follow-up was performed by nurses after 18 h, 48 h, 2 weeks and thereafter every month until stent dysfunction or the patient died. Outcomes were measured as follows: the patients reported urine and stool color, presence of fever and abdominal pain. Liver function tests and CRP were analyzed each time. The procedure time and complications were monitored. The follow-up was blinded to stent type. Results. The median patient age was 79 years (IQR: 66–83, R: 54–92), 59% were female and 85% had the gallbladder in situ. There was no difference between covered and uncovered stents in terms of procedure time (median: 30 min (20–38, R: 12–90) vs. 30 min (IQR: 20–42, R: 12–70)), stent patency (median: 153 days (IQR: 65–217; R: 20–609) vs. median of 127 days (IQR: 70–196; R: 18–486)) or patient survival (median: 154 days (IQR: 65–217; R: 21–609) vs 157 days (IQR: 70–273, R: 20–690)). Eighty-seven percent died with a patent covered and 83% with an uncovered stent (n.s.). Two early complications occurred (sepsis; pancreatitis), both with covered stents. Conclusion. There is no clinical difference between covered and uncovered biliary Hanaro SEMS. Both types are easily inserted with low complication rate and have long-term patency.
Evaluation of Artemisone Combinations in Aotus Monkeys Infected with Plasmodium falciparum

ABSTRACT Artemisone (single oral dose, 10 mg/kg of body weight) cured nonimmune Aotus monkeys of their Plasmodium falciparum infections when combined with mefloquine (single oral dose, 5 and 10 mg/kg but not 2.5 mg/kg). In combination with amodiaquine (20 mg/kg/day), artemisone (10 mg/kg/day) given orally for 3 days cured all infected monkeys. Three days of treatment with artemisone (30 mg/kg/day) and clindamycin (100 mg/kg/day) was also curative.
Shrinkability of ethylene vinyl acetate/polyurethane blends and their characterization

Heat shrinkability of the polymer, which depends on the elastic memory, is being utilized in various applications, mainly in the field of encapsulation. The elastic memory is introduced into the system in the form of an elastomeric phase. Here the blends of ethylene vinyl acetate and polyurethane were studied with reference to their shrinkability, introducing crosslinking in both the phases. It is found that with increase in elastomer content the shrinkage increased to a certain level and then decreased. With increase in cure time shrinkage is decreased. It is seen that high-temperature (HT) stretched samples showed higher shrinkage than room temperature (RT) stretched one. Generally, the crystallinity of the HT stretched sample is higher than that of low-temperature stretched sample, which is again higher than that of original sample. From high temperature differential scanning calorimetry it is found that with increase in PU content stability towards oxygen is increased and further high temperature processing decreases the initial degradation temperature but enhances the rate of degradation. From scanning electron microscopy it is seen that an HT stretched sample is more elongated than an RT stretched one. Copyright © 2000 John Wiley & Sons, Ltd.
Relationship between initial vancomycin concentration-time profile and nephrotoxicity among hospitalized patients.

BACKGROUND Data suggest that higher doses of vancomycin can increase the risk of nephrotoxicity. No study has been undertaken to determine the pharmacodynamic index (ie, the area under the curve [AUC] or the trough value) that best describes the relationship between vancomycin exposure and onset of nephrotoxicity. METHODS A retrospective study was conducted among patients who received vancomycin for a suspected or proven gram-positive infection during the period from 1 January 2005 through 31 December 2006 at Albany Medical Center Hospital. Patients were included in our study if they (1) were > or =18 years old, (2) had an absolute neutrophil count of > or =1000 cells/mm(3), (3) received vancomycin for >48 h, (4) had 1 vancomycin trough level collected within 96 h of vancomycin therapy, and (5) had a baseline serum creatinine level of <2.0 mg/dL. Patients were excluded if they (1) had a diagnosis of cystic fibrosis, (2) received intravenous contrast dye within 7 days of starting vancomycin or during therapy, or (3) required vasopressor support during therapy. Demographics, comorbid conditions, and treatment data were collected. The highest observed vancomycin trough value within 96 h of initiation of vancomycin therapy and the estimated vancomycin AUC were analyzed as measures of vancomycin exposure. The vancomycin AUC value from 0 to 24 h at steady state (in units of mg x h/L) for each patient was estimated by use of the maximum a posteriori probability Bayesian procedure in ADAPT II. Nephrotoxicity was defined as an increase in serum creatinine level of 0.5 mg/dL or 50%, whichever was greater, following initiation of vancomycin therapy. Logistic and Cox proportional hazards regression models identified the vancomycin pharmacodynamic index that best describes the relationship between vancomycin exposure and toxicity. RESULTS During the study period, 166 patients met the inclusion criteria. Both initial vancomycin trough values and 0-24-h at steady state AUC values were associated with nephrotoxicity in the bivariate analyses. However, the vancomycin trough value, modeled as a continuous variable, was the only vancomycin exposure variable associated with nephrotoxicity in the multivariate analyses. CONCLUSIONS The results indicate that a vancomycin exposure-toxicity response relationship exists. The vancomycin trough value is the pharmacodynamic index that best describes this association.
Recovering Missing Labels of Crowdsourcing Workers

Data sets collected from crowdsourcing platforms are well known for their cheap costs. But cheap costs may lead to low quality, i.e., labels may be incorrect or missing. Most of the existing work focuses on modeling the labeling errors of crowd workers, but missing labels can also cause problems when modeling the data. In this paper, we present an algorithm to predict the missing labels of crowd workers, in which we adopt thoughts from semi-supervised learning and utilize the particular consistency between crowd workers. We also define the consistency between workers by crowd labels and develop an algorithm to learn them from the data automatically. Experiments on both benchmark and real data show that our algorithm outperforms traditional semisupervised learning algorithms in predicting missing labels, and the recovered crowd labels are capable of predicting the ground truth and reflecting real properties of crowd workers.
A portability study on natural language call steering

In this paper we examine the portability of the vector-based call router to a new task involving calls to the operator in the UK. One component of the router was shown to require expert knowledge and hand-tuning: the stop word list. Stop word filtering involves replacing certain words with place markers and is necessary to reduce the number of features and parameters used by the classifier. Two specific approaches that eliminates the need for stop word filtering were investigated that led to comparable classification performance: (1) using trigram, bigram, and unigram features and using SVD to reduce the number of parameters, and (2) using only unigram features and applying discriminative training to boost the performance. After discriminative training, the classification error rate was reduced by 18-30% over the baseline unigram results. Increased robustness is demonstrated by a 24-48% reduction in error rate at 20% false rejection rate.
The Influence of External Forces on Wrist Proprioception

Proprioception combines information from cutaneous, joint, tendon, and muscle receptors for maintaining a reliable internal body image. However, it is still a matter of debate, in both neurophysiology and psychology, to what extent such body image is modified or distorted by a changing haptic environment. In particular, what is worth investigating is the contribution of external forces on our perception of body and joint configuration. The proprioceptive acuity of fifteen young participants was tested with a Joint Position Matching (JPM) task, performed with the dominant wrist under five different external forces, in order to understand to what extent they affect proprioceptive acuity. Results show that accuracy and precision in target matching do not change in a significant manner as a function of the loading condition, suggesting that the multi-sensory integration process is indeed capable of discriminating different sub-modalities of proprioception, namely the joint position sense and the sense of force. Furthermore, results indicate a preference for target undershooting when movements are performed in a viscous or high resistive force field, rather than passive or null fields in which subjects did not show any predominance for under/over estimation of their position.
Approaching cross-national comparisons of nursing home residents.

METHOD since the 1990 implementation of the US nursing home Resident Assessment Instrument (RAI), researchers in other nations have begun to use the RAI to assess institutionalized elders for payment, research, or planning purposes. We report comparative statistics representing institutionalized residents in seven nations, describing from several hundred to hundreds of thousands of residents. RESULTS significant differences are seen in age and length of stay, and in summary measures of physical and cognitive functioning and case-mix. Countries also differ in their homogeneity across nursing homes. CONCLUSION these differences strengthen the position that 'nursing home' does not provide a sound basis for cross-national comparisons, and should be replaced with resident-specific descriptors. This also suggests that cross-national comparisons need to adjust at the level of the individual resident for differences in resident populations.
Relationship Between Collateral Circulation and Successful Myocardial Reperfusion in Acute Myocardial Infarction: A Subanalysis of the PREMIAR Trial

The aim of this study was to determine whether the presence of collateral circulation had a beneficial effect following primary angioplasty. In all, 114 patients who underwent primary angioplasty were included. Patients with collateral circulation had lower basal ST-segment deviation (P = .004), white cell count ( P = .001), peak creatine kinase (P = .001), and regional wall motion score values (P = .03) than patients without collateral circulation. After the procedure, the group with collaterals was associated with higher rates of normal myocardial blush, complete ST resolution, and shorter time to stable ST-recovery. Multivariable logistic analysis identified the presence of collateral circulation as independent predictor of normal myocardial blush (adjusted odds ratio = 3.98, 95% confidence interval, 1.12-14.09; P = .033) and rapid reperfusion (time to stable ST-segment recovery <7 minutes, adjusted odds ratio = 4.0, 95% confidence interval, 1.57-10.20; P = .004). The presence of collateral circulation has a protective effect on infarct size, resulting in faster reperfusion.
Do Automatically Generated Unit Tests Find Real Faults? An Empirical Study of Effectiveness and Challenges (T)

Rather than tediously writing unit tests manually, tools can be used to generate them automatically - sometimes even resulting in higher code coverage than manual testing. But how good are these tests at actually finding faults? To answer this question, we applied three state-of-the-art unit test generation tools for Java (Randoop, EvoSuite, and Agitar) to the 357 real faults in the Defects4J dataset and investigated how well the generated test suites perform at detecting these faults. Although the automatically generated test suites detected 55.7% of the faults overall, only 19.9% of all the individual test suites detected a fault. By studying the effectiveness and problems of the individual tools and the tests they generate, we derive insights to support the development of automated unit test generators that achieve a higher fault detection rate. These insights include 1) improving the obtained code coverage so that faulty statements are executed in the first instance, 2) improving the propagation of faulty program states to an observable output, coupled with the generation of more sensitive assertions, and 3) improving the simulation of the execution environment to detect faults that are dependent on external factors such as date and time.