LLukas22/scidocs huggingface dataset:
Sorafenib plus dacarbazine in solid tumors: a phase I study with dynamic contrast-enhanced ultrasonography and genomic analysis of sequential tumor biopsy samples

Purpose Improved prognostic accuracy for treatment response and a wider understanding of drug effects in humans are crucial for enhancing the utility of sorafenib and other promising targeted therapies. We developed a strategy of global genomic investigation of sequential tumor biopsy samples at baseline and 21 days post treatment, and applied this approach in a phase I study of sorafenib plus dacarbazine in patients with solid tumors. The objective of this study was also to validate functional parameters of DCE-US as surrogate markers to predict earlier response. Experimental design Patients received 21-day cycles of oral sorafenib, 400 mg twice daily and dacarbazine, 1,000 mg/m2 in a 1-h intravenous infusion on day 1. Efficacy was assessed using response evaluation criteria in solid tumors. Sequential biopsy samples (baseline and day 21) were obtained from the same tumor. Changes from baseline in global gene expression (GE) measured by genomic microarrays and in tumor vascularity at baseline, D8, D21, D 42 and every 2 cycles using dynamic contrast-enhanced ultrasonography (DCE-US) were analyzed for patients with and without a clinical response to treatment at 3 months. Results Among 23 patients evaluable for treatment efficacy, 17 were eligible for gene expression and DCE-US analyses. One patient achieved a partial response; 14 exhibited stable disease. Ten patients were defined as exhibiting stable disease (SD) and 7, progressive disease (PD) at 3 months. Genomic analyses identified a 237-gene signature that distinguished SD from PD at 3 months. Of note, CDK4 overexpression and PDGFR downregulation were associated with PD. Functional parameters of DCE-US representing the blood volume at baseline, day 8, and day 21 were correlated with disease progression at 3 months. Conclusions This novel approach of sequential investigations in a phase I trial was feasible, detecting early changes in gene expression and tumor vascularity evaluated using DCE-US that may be predictive of clinical outcome.
Radiation measurements in the Chiba Metropolitan Area and radiological aspects of fallout from the Fukushima Dai-ichi Nuclear Power Plants accident.

Large amounts of radioactive substances were released into the environment from the Fukushima Dai-ichi Nuclear Power Plants in eastern Japan as a consequence of the great earthquake (M 9.0) and tsunami of 11 March 2011. Radioactive substances discharged into the atmosphere first reached the Chiba Metropolitan Area on 15 March. We collected daily samples of air, fallout deposition, and tap water starting directly after the incident and measured their radioactivity. During the first two months maximum daily concentrations of airborne radionuclides observed at the Japan Chemical Analysis Center in the Chiba Metropolitan Area were as follows: 4.7 × 10(1) Bq m(-3) of (131)I, 7.5 Bq m(-3) of (137)Cs, and 6.1 Bq m(-3) of (134)Cs. The ratio of gaseous iodine to total iodine ranged from 5.2 × 10(-1) to 7.1 × 10(-1). Observed deposition rate maxima were as follows: 1.7 × 10(4) Bq m(-2) d(-1) of (131)I, 2.9 × 10(3) Bq m(-2) d(-1) of (137)Cs, and 2.9 × 10(3) Bq m(-2) d(-1) of (134)Cs. The deposition velocities (ratio of deposition rate to concentration) of cesium radionuclides and (131)I were detectably different. Radioactivity in tap water caused by the accident was detected several days after detection of radioactivity in fallout in the area. Radiation doses were estimated from external radiation and internal radiation by inhalation and ingestion of tap water for people living outdoor in the Chiba Metropolitan Area following the Fukushima accident.
Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation

The specific post-translational modifications to histones influence many nuclear processes including gene regulation, DNA repair and replication. Recent studies have identified effector proteins that recognize patterns of histone modification and transduce their function in downstream processes. For example, histone acetyltransferases (HATs) have been shown to participate in many essential cellular processes, particularly those associated with activation of transcription. Yeast SAGA (Spt-Ada-Gcn5 acetyltransferase) and SLIK (SAGA-like) are two highly homologous and conserved multi-subunit HAT complexes, which preferentially acetylate histones H3 and H2B and deubiquitinate histone H2B. Here we identify the chromatin remodelling protein Chd1 (chromo-ATPase/helicase-DNA binding domain 1) as a component of SAGA and SLIK. Our findings indicate that one of the two chromodomains of Chd1 specifically interacts with the methylated lysine 4 mark on histone H3 that is associated with transcriptional activity. Furthermore, the SLIK complex shows enhanced acetylation of a methylated substrate and this activity is dependent upon a functional methyl-binding chromodomain, both in vitro and in vivo. Our study identifies the first chromodomain that recognizes methylated histone H3 (Lys 4) and possibly identifies a larger subfamily of chromodomain proteins with similar recognition properties.
Maximum power point tracking using adaptive fuzzy logic control for grid-connected photovoltaic system

This paper proposes a method of maximum power point tracking using adaptive fuzzy logic control for grid-connected photovoltaic systems. The system is composed of a boost converter and a single-phase inverter connected to a utility grid. The maximum power point tracking control is based on adaptive fuzzy logic to control a switch of a boost converter. Adaptive fuzzy logic controllers provide attractive features such as fast response, good performance. In addition, adaptive fuzzy logic controllers can also change the fuzzy parameter for improving the control system. The single phase inverter uses predictive current control which provides current with sinusoidal waveform. Therefore, the system is able to deliver energy with low harmonics and high power factor. Both conventional fuzzy logic controller and adaptive fuzzy logic controller are simulated and implemented to evaluate performance. Simulation and experimental results are provided for both controllers under the same atmospheric condition. From the simulation and experimental results, the adaptive fuzzy logic controller can deliver more power than the conventional fuzzy logic controller. q 2005 Published by Elsevier Ltd.
Surface finish of precision machined advanced materials

This paper studies the surface finish and integrity of glass, silicon, some advanced ceramics and aluminum-based metal matrix composites (MMCs) reinforced with ceramic particles, precision machined by various machining processes. The studies revealed that grinding/lapping operations using inexpensive machine tools can produce ductile streaks on glass and silicon surfaces under good grinding/lapping conditions. This resulted in significantly shortened polishing time to secure an acceptable surface finish. If there are several processes to manufacture a lens, each preceding process is very important for the successive processes. In order to reduce the total manufacturing time, it is preferable to obtain better ground/lapped surfaces with as many ductile streaks as possible in order to reduce the polishing time. Toroidal SiC surfaces ground with flat-face cup wheels indicated 100% ductile machining, and did not require polishing. Ground ZrO2 showed a numerous ductile streaks. Plastic deformation was the major mechanism of material removal at high wheel speeds. Grinding of aluminum-based MMCs reinforced with Al2O3 or SiC particles using a 3000 grit diamond wheel at depths of grinding of 1 and 0.5 mm produced many ductile streaks on the Al2O3 and SiC particles, respectively. There was almost no sub-surface damage. The machines used for the experiments reported in this paper are not expensive ultra-precision machines. # 2002 Elsevier Science B.V. All rights reserved.
Comparison of 9-month angiographic outcomes of Resolute zotarolimus-eluting and everolimus-eluting stents in a real world setting of coronary intervention in Korea

BACKGROUND
Clinical outcomes of new-generation drug-eluting stents (DES), Everolimus-eluting stent (EES) or Resolute zotarolimus-eluting stent (R-ZES), have been reported. However, angiographic follow-up data of new-generation DES are limited, especially in Asians. We investigated the angiographic and clinical outcomes of EES and R-ZES in a real-world setting of Korean patients.


METHODS
Angiographic and clinical outcomes of 679 patients (866 lesions) who had been treated with EES or R-ZES from Jun 2008 to May 2010 were evaluated. The primary analysis was to compare in-segment late loss at 9 months and the secondary analyses were to compare the clinical outcomes.


RESULTS
In-segment late loss at 9-month follow-up angiography was 0.23 ± 0.52 mm for EES and 0.29 ± 0.64 mm for R-ZES (p = 0.248). In addition, the rate of binary restenosis did not show between-group differences (5.8% vs. 6.8% for EES and R-ZES, respectively, p = 0.716). During a median follow-up of 33 months, there were no significant differences in Kaplan-Meier estimates of target lesion failure (TLF) (7.5% vs. 7.9% for EES and R-ZES, respectively, p = 0.578) and patient-oriented composite outcomes (POCO including all-cause death, any myocardial infarction, and any revascularization, 22.8% vs. 20.1%, p = 0.888). The adjusted hazard ratios for TLF and POCO were 0.875 (95% CI 0.427 - 1.793; p = 0.715) and 1.029 (95% CI 0.642 - 1.650; p = 0.904), respectively, for EES over R-ZES in the propensity score matched group analysis.


CONCLUSIONS
In Korean patients undergoing new-generation DES implantation for coronary artery disease, EES and R-ZES showed similar angiographic outcomes at 9 months and comparable clinical outcomes during 2.8 years of median follow-up.
Does concomitant diabetes affect treatment responses in overactive bladder patients?

AIMS
To compare the efficacy and tolerability of a muscarinic receptor antagonist, darifenacin, in the treatment of overactive bladder (OAB) patients with concomitant diabetes as compared with those without comorbidities.


METHODS
Post hoc exploratory analysis of a published, large, non-interventional study in OAB patients treated with darifenacin including 532 diabetics and 1315 controls. Associations of diabetes with treatment responses were evaluated by multiple regression models.


RESULTS
Diabetics (largely type 2 patients) and controls differed in baseline age, body weight, duration of OAB symptoms and presence of co-medications. However, they exhibited similar OAB symptom episode frequency and problem rating and received similar starting doses of darifenacin. Presence of diabetes was associated with a significantly smaller reduction of OAB symptoms, but the effect attributable to diabetes was small relative to the overall treatment response. The presence of diabetes was not associated with differences in tolerability.


DISCUSSION AND CONCLUSIONS
We conclude that a muscarinic receptor antagonist has comparable efficacy and tolerability in the treatment of OAB patients with and without concomitant diabetes.
Phenotypic approaches to drought in cassava: review

Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12-18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding.
Effect of arcing on DC flashover performance of contaminated porcelain insulators for various suspension patterns at high altitudes

This paper presents an analysis of the arcing and flashover performance of contaminated dc insulators of various suspension patterns at high altitudes (1970 m). The experiments tested two types of dc insulators, a bell-type insulator and a tri-shed suspension insulator. The experimental results show that dc arcs play an important role in the flashover performance since they levitate more easily from the porcelain surfaces at high altitudes than at sea level. For heavily contaminated insulators, the relationship between the insulator length and the flashover voltage per insulator unit is affected by the arc development path, and is lower for shorter insulator strings (10 to 20 insulator units). With a non-uniform contamination distribution between the top and bottom insulator surfaces, the arcs propagate close to the insulator surface, resulting in a higher flashover voltage than with uniform contamination. The Y-string configuration appears to lead to much lower flashover voltages than in I- and V-string insulators. With the latter, the arc propagation path is greatly influenced by the angle between the two insulator strings with the flashover voltages for both bell-type and tri-shed insulators increasing with the angle but apparently due to different mechanisms. Experimental results indicate that the bell-type insulator has better flashover characteristic; than the tri-shed insulator.
Adsorption of Heavy Metal ( Cu 2 + , Ni 2 + and Zn 2 + ) from Synthetic Waste Water by Tea Waste Adsorbent

Industrial waste constitutes the major source of various kinds of metal pollution in natural water. There are at least 20 metals which cannot be degraded or destroyed. The important toxic metals are Cu, Ni and Zn. There are numerous methods currently employed to remove and recover the metals from our environment and many physicochemical methods have been proposed for their removal from wastewater. Adsorption is one of the alternatives for such cases and is an effective purification and separation technique used in industry especially in water and wastewater treatments. Cost is an important parameter for comparing the adsorbent materials. Therefore, there is increasing research interest in using alternative low-cost adsorbents. The use of tea waste as the low-cost adsorbents was investigated as a replacement for current costly methods of removing heavy metal ions from aqueous solutions. The experiment results showed that maximum removal of Nickel ion by tea waste is 94% and for Copper & Zinc ion are 89% & 90% respectively at optimum condition.
Procjena dentalne starosti djece u razvoju: usporedba između različitih europskih zemalja Dental Age Estimation of Growing Children: Comparison Among Various European Countries

Adresa za dopisivanje Roberto Camariere Institut za sudsku medicinu Sveučilišta u Macerati Via Don Monzoni 9 62100 Macerata Italija Tel: +390733258625 Fax: +3907332582635 r.cameriere@unimc.it Sažetak Procjena dobi djece temeljno je pitanje u sudskoj medicini, pedijatrijskoj endokrinologiji i ortodontskom liječenju. Za to se koristi nekoliko metoda, uključujući i onu na osnovi razvoja kostiju i zuba. Budući da je nekoliko autora ustanovilo da se dentalne metode mogu razlikovati prema točnosti procjene, ovaj se rad temelji na poboljšanjima metode koju su razvili Cameriere i suradnici te ih proširuje na veći uzorak djece iz nekoliko europskih regija 505 iz Italije, 304 s Kosova i 291 iz Slovenije. Također se ispitala učinkovitost metode u situacijama kada se različite populacije analiziraju zajedno. Koefi cijenti korelacije procjenjivali su se između dobi i predvidivih varijabli. Statistička analiza obavljena je u statističkom programu S-PLUS 6 (SPLUS 6.1 za Windowsov operativni sustav Professional Edition, Release 1). Razina znatnosti postavljena je na 5%. Statistička analiza pokazala je da spol, zbroj normalno otvorenih apeksa i broj zuba s potpuno razvijenim korjenovima znatno utječu na procjenu starosti. Pripadnost različitim europskim regijama nije utjecala na parametre modela. Ključne riječi određivanje starosti pomoću zuba; dentalna radiografi ja; sudska stomatologija; regresijska analiza 1 Institut za sudsku medicinu Sveučilišta u Macerati, Macerata, Italija Institute of Legal Medicine,University of Macerata, Macerata, Italy 2 Institut za mikrobiologiju i biomedicinske znanosti Politehničkog sveučilišta pokrajine Marche, Macerata, Italija Institute of Microbiology and Biomedical Sciences, Polytechnical University of Marche, Macerata, Italy 3 Institut za sudsku medicinu Sveučilišta u Ljubljani, Slovenija Institute of Forensic Medicine, University of Ljubljana, Slovenia 4 Zavod za ortodonciju Sveučilišta u Prištini, Priština, Kosovo Department of Orthodontics, University of Prishtina, Prishtina, Kossovo
Myocardial Performance in Asphyxiated Full-Term Infants Assessed by Doppler Tissue Imaging

The aim of this study was to assess myocardial performance of full-term infants with perinatal asphyxia using Doppler tissue imaging (DTI) and to correlate it with serum cardiac troponin T (cTnT) concentrations. Twenty-five asphyxiated and 20 nonasphyxiated term infants were investigated. Serum cTnT concentrations were measured between 12 and 24 h of life. Conventional two-dimensional Doppler echocardiography and DTI were done during the first 72 h of life. Right ventricular (RV) and left ventricular (LV) Tei indexes were significantly higher in asphyxiated neonates (mean ± SD: 0.45 ± 0.05 vs. 0.28 ± 0.05, P < 0.001 and 0.51 ± 0.04 vs. 0.38 ± 0.04, P < 0.001, respectively). Mitral and tricuspid systolic (Sm) velocities were significantly lower in asphyxiated neonates (mean ± SD: 5.06 ± 0.89 vs. 6.89 ± 0.94 cm/s, P < 0.001 and 5.78 ± 0.58 vs. 6.69 ± 0.87 cm/s, P < 0.001, respectively). cTnT concentrations were significantly higher in asphyxiated neonates [median (range): 0.17 (0.05–0.23) vs. 0.03 (0–0.07) μg/l, P < 0.001)], and they correlated positively with the LV Tei index (r = 0.67, P < 0.001) and the RV Tei index (r = 0.68, P < 0.001) and negatively with the mitral systolic (Sm) velocity (r = –0.68, P < 0.001) and tricuspid systolic (Sm) velocity (r = –0.41, P = 0.01). A higher cTnT was a significant predictor of mortality, whereas fractional shortening (FS) and DTI measurements did not show any significant predictive value. The DTI technique appears to be more sensitive than conventional echocardiography in the early detection of myocardial dysfunction induced by perinatal asphyxia in full-term infants.
A phase I pharmacologic and pharmacogenetic trial of sequential 24-hour infusion of irinotecan followed by leucovorin and a 48-hour infusion of fluorouracil in adult patients with solid tumors.

PURPOSE
In preclinical studies, sequential exposure to irinotecan (CPT-11) then fluorouracil (5-FU) is superior to concurrent exposure or the reverse sequence; a 24-hour infusion of CPT-11 may be better tolerated than shorter infusions.


EXPERIMENTAL DESIGN
CPT-11 was first given at four levels (70-140 mg/m(2)/24 hours), followed by leucovorin 500 mg/m(2)/0.5 hours and 5-FU 2,000 mg/m(2)/48 hours on days 1 and 15 of a 4-week cycle. 5-FU was then increased in three cohorts up to 3,900 mg/m(2)/48 hours.


RESULTS
Two patients had dose-limiting toxicity during cycle 1 at 140/3,900 of CPT-11/5-FU (2-week delay for neutrophil recovery; grade 3 nausea despite antiemetics); one of six patients at 140/3,120 had dose-limiting toxicity (grade 3 diarrhea, grade 4 neutropenia). Four of 22 patients with colorectal cancer had partial responses, two of which had prior bolus CPT-11/5-FU. The mean 5-FU plasma concentration was 5.1 micromol/L at 3,900 mg/m(2)/48 hours. The end of infusion CPT-11 plasma concentration averaged 519 nmol/L at 140 mg/m(2)/24 hours. Patients with UDP-glucuronosyltransferase (UGT1A1; TA)6/6 promoter genotype had a lower ratio of free to glucuronide form of SN-38 than in patients with >/=1 (TA)7 allele. Thymidylate synthase genotypes for the 28-base promoter repeat were 2/2 (13%), 2/3 (74%), 3/3 (13%); all four responders had a 2/3 genotype.


CONCLUSIONS
Doses (mg/m(2)) of CPT-11 140/24 hours, leucovorin 500/0.5 hours and 5-FU 3,120/48 hours were well tolerated.
Detection of Microbial Translocation in HIV and SIV Infection Using the Limulus Amebocyte Lysate Assay is Masked by Serum and Plasma

OBJECTIVE
Microbial translocation (MT) is thought to be a major contributor to the pathogenesis of HIV-related immune activation, and circulating lipopolysaccharide (LPS) from gram-negative bacteria is the principle measurement of this process. However, related research has been impeded by inconsistent LPS test results.


METHODS
Specimens were obtained from HIV-infected adults enrolled in the PEARLS study (ACTG A5175) and HIV-HCV co-infected participants enrolled in a study of liver disease staging using MRI elastography. Pig-tailed macaque specimens were obtained from SIV-infected and -uninfected animals. Samples were tested for LPS using the LAL assay with diazo-coupling modifications to improve sensitive detection.


RESULTS
When exogenous LPS was added to macaque plasma, >25% inhibition of LPS detection was found in 10/10 (100%) samples at 20% plasma concentration compared to control; in contrast 5/10 (50%) samples at 2% plasma concentration (p = 0.07) and 0/10 (0%) at 0.1% plasma concentration (p = 0.004) showed >25% inhibition of LPS detection. Similarly, when LPS was added to human serum, >25% inhibition of LPS detection was found in 5/12 (42%) of samples at 2% serum concentration compared to control, while 0/12 (0%) of samples in 0.1% serum showed >25% inhibition of LPS detection (p = 0.07). Likewise, LPS detection in human sera without exogenous LPS was improved by dilution: LPS was detected in 2/12 (17%) human samples in 2% serum, ranging from 3,436-4,736 pg/mL, compared to 9/12 (75%) samples in 0.1% serum, ranging from 123 pg/mL -60,131 pg/mL (p = 0.016). In a separate validation cohort of HIV-HCV co-infected participants sampled at two different times on the same day, LPS measured in 0.2% plasma and with diazo-coupling was closely correlated between the first and second samples (R = 0.66, p<0.05).


CONCLUSIONS
Undiluted serum and plasma mask LPS detection. The extent of MT may be substantially underestimated.