Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy and safety of EUS-guided gastroenterostomy for benign and malignant gastric outlet obstruction: a systematic review and meta-analysis

Abstract Background and study aims Endoscopic ultrasound-guided gastroenterostomy (EUS-GE) is a novel endoscopic procedure designed to facilitate sustained luminal patency in patients with gastric outlet obstruction. The primary aim of this study was to evaluate the efficacy and safety of EUS-GE for treatment of gastric outlet obstruction. Methods Searches of PubMed, EMBASE, Web of Science, and Cochrane Library databases were performed through April 2019. Patients with benign and malignant gastric outlet obstruction were included. Measured outcomes included: immediate technical and clinical success as well as rate of serious adverse events (AEs). Heterogeneity was assessed with Cochran Q test and I 2 statistics. Publication bias was ascertained by funnel plot and Egger regression testing. Results A total of five studies (n = 199 patients; 45.73 % male) were included in this study. Four retrospective studies and one prospective study were analyzed. Mean age of patients that underwent the EUS-GE procedure was 64.52 ± 1.37 years with a pooled mean follow-up period of 4.32 ± 1.65 months. In 21 % of patients (n = 43), gastric outlet obstruction was due to benign causes. Immediate technical success was 92.90 % (95 % CI; 88.26 – 95.79; I2 = 0.00 %) and reported in all studies. The clinical success rate of EUS-GE was 90.11 % (95 % CI; 84.64 – 93.44; I2 = 0.00 %). Serious AEs occurred in 5.61 % (95 % CI; 2.87 – 10.67; I2 = 1.67 %) of cases and were related to peritonitis, perforation, bleeding, and abdominal pain. Re-intervention rate was 11.43 % (95 % CI; 7.29 – 17.46; I2 = 17.38 %). Conclusions EUS-GE appears to provide an effective and safe minimally invasive alternative for treatment of benign and malignant gastric outlet obstruction.
Multi-platform Affinity Proteomics Identify Proteins Linked to Metastasis and Immune Suppression in Ovarian Cancer Plasma

A central reason behind the poor clinical outcome of patients with high-grade serous carcinoma (HGSC) of the ovary is the difficulty in reliably detecting early occurrence or recurrence of this malignancy. Biomarkers that provide reliable diagnosis of this disease are therefore urgently needed. Systematic proteomic methods that identify HGSC-associated molecules may provide such biomarkers. We applied the antibody-based proximity extension assay (PEA) platform (Olink) for the identification of proteins that are upregulated in the plasma of OC patients. Using binders targeting 368 different plasma proteins, we compared 20 plasma samples from HGSC patients (OC-plasma) with 20 plasma samples from individuals with non-malignant gynecologic disorders (N-plasma). We identified 176 proteins with significantly higher levels in OC-plasma compared to N-plasma by PEA (p < 0.05 by U-test; Benjamini-Hochberg corrected), which are mainly implicated in immune regulation and metastasis-associated processes, such as matrix remodeling, adhesion, migration and proliferation. A number of these proteins have not been reported in previous studies, such as BCAM, CDH6, DDR1, N2DL-2 (ULBP2), SPINT2, and WISP-1 (CCN4). Of these SPINT2, a protease inhibitor mainly derived from tumor cells within the HGSC microenvironment, showed the highest significance (p < 2 × 10−7) similar to the previously described IL-6 and PVRL4 (NECTIN4) proteins. Results were validated by means of the aptamer-based 1.3 k SOMAscan proteomic platform, which revealed a high inter-platform correlation with a median Spearman ρ of 0.62. Likewise, ELISA confirmed the PEA data for 10 out of 12 proteins analyzed, including SPINT2. These findings suggest that in contrast to other entities SPINT2 does not act as a tumor suppressor in HGSC. This is supported by data from the PRECOG and KM-Plotter meta-analysis databases, which point to a tumor-type-specific inverse association of SPINT2 gene expression with survival. Our data also demonstrate that both the PEA and SOMAscan affinity proteomics platforms bear considerable potential for the unbiased discovery of novel disease-associated biomarkers.
A metrological scanning probe microscope based on a quartz tuning fork detector

We give an overview of the design of a metrological Scanning Probe Microscope (mSPM) currently under development at the National Measurement Institute Australia (NMIA) and report on preliminary results on the implementation of key components. The mSPM is being developed as part of the nanometrology program at NMIA and will provide the link in the traceability chain between dimensional measurements made at the nanometre scale and the realization of the SI metre at NMIA. The instrument is based on a quartz tuning fork (QTF) detector and will provide a measurement volume of 100 μm × 100 μm × 25 μm with a target uncertainty of 1 nm for the position measurement. Characterization results of the nanopositioning stage and the QTF detector are presented along with an outline of the method for tip mounting on the QTFs. Initial imaging results are also presented.
VOLATILITY SPILLOVER EFFECTS IN THE EXTRA VIRGIN OLIVE OIL MARKETS OF THE MEDITERRANEAN

The objective of this study is to assess the existence and magnitude of volatility spillovers between the extra virgin olive oil markets of Italy, Spain and Greece. These three Mediterranean countries are responsible for 95% of olive oil production within the European Union and they account for more than 50% of olive oil exports worldwide. In order to measure the degree of volatility transmission between these countries we estimate a vector error correction model along with the BEKK parameterization of a Multivariate Generalized Conditional Autoregressive Heteroskedasticity (M-GARCH) model. The empirical results reveal the presence of ARCH and GARCH effects suggesting this way the existence of volatility spillovers between the extra virgin olive oil markets of Italy, Greece and Spain. ARCH effects are the biggest in magnitude for the market between Spain and Italy. GARCH effects are the biggest in magnitude for the market between Greece and Italy.
Administration Timing Is the Best Clinical Outcome Predictor for Adalimumab Administration in Crohn's Disease

Biological intervention for Crohn's Disease (CDs) patients, mainly using anti-TNF antibodies, is often an efficient therapeutic solution. Nonetheless, data defining the administration timing to maximize the chances of clinical remission are lacking. The objective of this “real-life” retrospective study was to evaluate if early Adalimumab (ADA) administration (<12 months) was an efficient strategy to improve patients' clinical outcome. This single center study included 157 CD patients, of which 80 received the first ADA administration within the first 12 months from the diagnosis. After 1 year of therapy, clinical remission was observed in 50.32% of patients, mucosal healing in 37.58%. Clinical remission was observed in 66.25% of the early ADA administration patients vs. 33.77% of the late (>12 months) (p < 0.001); mucosal healing was observed in 53.75% of the early vs. 20.78% of the late (p < 0.001). Dose escalation was required for 30.00% of the early vs. 66.23% of the late (<0.01). In the early ADA administration group, 7.50% patients were considered non-responders at the end of the follow-up vs. 22.08% patients in the late administration group. These findings highlighted that early ADA administration (within 1 year of diagnosis) improves the clinical response and mucosal healing, and reduces the loss of response rate and need for dose escalation.
Pathogenicity of Clinical OXA-48 Isolates and Impact of the OXA-48 IncL Plasmid on Virulence and Bacterial Fitness

OXA-48 is the most common carbapenemase in Enterobacterales in Germany and one of the most frequent carbapenemases worldwide. Several reports have associated blaOXA–48 with a virulent host phenotype. To challenge this hypothesis, 35 OXA-48-producing clinical isolates of Escherichia coli (n = 15) and Klebsiella pneumoniae (n = 20) were studied in vitro, in vivo employing the Galleria mellonella infection model and by whole-genome sequencing. Clinical isolates belonged to 7 different sequence types (STs) in E. coli and 12 different STs in K. pneumoniae. In 26/35 isolates blaOXA–48 was located on a 63 kb IncL plasmid. Horizontal gene transfer (HGT) to E. coli J53 was high in isolates with the 63 kb IncL plasmid (transconjugation frequency: ∼103/donor) but low in isolates with non-IncL plasmids (<10–6/donor). Several clinical isolates were both highly cytotoxic against human cells and virulent in vivo. However, 63 kb IncL transconjugants generated from these highly virulent isolates were not more cytotoxic or virulent when compared to the recipient strain. Additionally, no genes associated with virulence were detected by in silico analysis of OXA-48 plasmids. The 63 kb plasmid was highly stable and did not impair growth or fitness in E. coli J53. In conclusion, OXA-48 clinical isolates in Germany are diverse but typically harbor the same 63 kb IncL plasmid which has been reported worldwide. We demonstrate that this 63 kb IncL plasmid has a low fitness burden, high plasmid stability and can be transferred by highly efficient HGT which is likely the cause of the rapid dissemination of OXA-48 rather than the expansion of a single clone or gain of virulence.
Evaluation of biomass activity in membrane bioreactors by means of respirometric techniques

The paper reports the main results of a respirometric experimental survey carried out on several membrane bioreactor pilot plants, characterized by different pilot plant layouts as well as operational conditions. The main aim was to assess the influence of specific conditions on biokinetic/stoichiometric parameters. In particular, the respirometric tests were specifically aimed at investigating the activity of both heterotrophic and autotrophic bacterial species. The achieved results showed that the plant configuration and the features of the feeding wastewater and operational conditions determine significant variation of the kinetic coefficients. The respirometric analysis was confirmed to be a simple and effective tool for the evaluation of the actual biomass kinetic parameters, to be used in mathematical models for the design phase as well as for monitoring the biomass viability during plant operations.
Analysis of Genetic Structure of Huchen (Hucho Hucho) in Serbia Inferred From Mitochondrial and Nuclear DNA

Abstract The purpose of this study was to assess the genetic diversity of Serbian huchen and provide guidelines for conservation and management. Fourteen huchen individuals were collected from six localities. For all individuals the mitochondrial DNA control region and the NADH1 gene were sequenced, and two microsatellite loci were genotyped. Sequencing of two mtDNA loci showed the presence of the same haplotypes (Hh_CR_1 and Hh_ND1_1) in all investigated specimens and the complete absence of genetic variability at inter- and intra-populational level. However, analyzed individuals from Serbia have the largest number of control region repeats (average 8.7) compared to all other huchen populations from the Danube basin. Microsatellite data show that the most of Serbian huchens were placed in the “eastern” cluster except one individual from the Drina River which clustered with “western” samples, most likely a consequence of stocking. In spite of only two loci used, four unique alleles found in the studied Serbian and Drina basin population indicate that the Danube basin may possess more region specific alleles than previously thought, which could be of great importance for efficient species management in the future. Abstract Cilj ovoga rada je bio da se izvrši procena genetičkog diverziteta mladice u Srbiji, i da se na osnovu dobijenih rezultata daju preporuke za buduće očuvanje i upravljanje fondom mladice. Za ovu svrhu sakupljeno je 14 jedinki sa šest lokaliteta. Za sve sakupljene jedinke sekvencirana je kontrolna regija, NADH1 gen mitohondijske DNK i genotipizirana su dva mikrosatelitska lokusa. Sekvenciranjem dva mtDNK lokusa utvrđeno je prisustvo istih haplotipova (Hh_CR_1 i Hh_ND1_1) kod svih ispitanih jedinki, odnosno, potpuno odsustvo genetičke varijabilnosti na inter- i intra-populacionom nivou. Međutim, analizirane jedinke iz Srbije karakterišu se najvećim brojem ponovaka kontrolne regije (prosečno 8,7), u poređenju sa svim ostalim populacijama mladice iz dunavskog sliva. Analizom mikrosatelitskih podataka, utvrđeno je da se gotovo sve jedinke iz Srbije svrstavaju u “istočnu” grupu, izuzev jedne jedinke iz Drine, koja je svrstana sa “zapadnim” uzorcima, što je najverovatnije posledica poribljavanja. Kod analiziranih jedinki sa teritorije Srbije i iz celokupnog sliva Drine pronađena su četiri jedinstvena alela, uprkos analizi samo dva mikrosatelitska lokusa. Dobijeni rezultati ukazuju da dunavski sliv može posedovati više regionalno specifičnih alela nego što se ranije smatralo, što bi moglo biti od velikog značaja za uspešno upravljanje fondom mladice u budućnosti.
Identification of New Alleles in Salt Tolerant Rice Germplasm Lines through Phenotypic and Genotypic Screening

The present study investigated eight rice lines (Rupsal, Nagalmutha, Polai, Ravana, Marishal, Talmugra, Kamini and Raspanjar) collected from coastal region of eastern India for salinity tolerance through phenotypic and genotypic screening. Among these, three rice lines as highly tolerant (Talmugra, Marishal and Kamini), three tolerant (Rupsal, Polai and Raspanjar) and two moderately tolerant (Ravana and Nagalmutha) to salt stress were identified in phenotypic screening. Pokkali was categorized as tolerant under salinity condition (12 EC dS m -1 ). In PCR screening using microsatellite (SSR) markers located within Saltol locus, we documented new allelic pattern in selected highly tolerant and tolerant genotypes with RM8094 marker as compared to Pokkali. Besides, another marker RM10694 was found to associate with selection of salinity tolerant genotypes similar to Pokkali. In gene expression studies, no significant difference linked with abscisic acid (ABA), calciumdependent proteins kinase (CDPK), ionic and osmotic signaling pathways in salinity tolerant genotypes was found as compared to sensitive line (IR29). Induction of AP37 gene expression differentiated Kamini and Marishal genotypes from other tolerant and sensitive lines. The chlorophyll and protein contents were maintained in highly tolerant genotypes (Marishal, Kamini and Talmugra) as compared to sensitive one (IR29). Among agronomic traits, selected rice lines recorded to have significant morphological features such as plant height, tiller number, leaf length and width in order to tolerate salt stress. Genetic diversity analysis revealed that, highly tolerant genotypes showed distant relationship with Pokkali at genetic level. © 2016 Friends Science Publishers
Characterization and evaluation of volatile compounds of three grape varieties ( Vitis labrusca ) from the region of Bento Gonçalves – RS

In grape must, the aroma is an indication of adequate conservation status. It is able to indicate losses due to thermal degradation, besides representing a great contribution in the properties of the sensorial quality of the grape juices most appreciated by consumers. This study identified the volatile compounds in different must cultivars of Vitis labrusca grapes. The volatile composition was evaluated by the solid phase microextraction method (SPME), using the polydimethylsiloxane/divinylbenzene fiber (PDMS/DVB). The separation and identification of the volatile compounds were carried out through gas chromatography by mass spectrometry (GC-MS). The results showed the identification of forty-four compounds belonging to the following chemical classes: carboxylic acids, alcohol, aldehydes, ketones, furans esters and terpenes. The class of esters was the most numerous compounds identified and is largely responsible for the fresh and fruity aroma of the tested musts. Solid-phase microextraction proved to be a reproducible, sensitive and fast-response technique for the identification of chemical biomarkers in musts of different grape cultivars.
Modelling approaches for addressing complexity in plant health management

Harmful organisms affect the quality and quantity of food production. In a world of increasing changes in climatic, economic and social conditions, the design of effective measures against these organisms requires more accurate information. Mathematical models provide a scientific and quantitative language to describe the complex relationships that causes pest outbreaks. With the goal of analysing options to deal with this complexity, we discuss different mathematical approaches to modelling. The best model to support plant protection decisions will vary with each situation. Mathematical models range from very simple correlations between events to complex comprehensive systems of differential equations used to represent the dynamics of processes. Large-scale scenarios at the national or continental level can be supported adequately with simple, static and general models. Analytical or descriptive dynamic models are the best options to support pest management in well-defined regions or locations with little variation in external factors. Explanatory dynamic models are needed when great variations in pest behaviour are expected as a result of higher-order interactions with the host and the environment. If necessary, a quantitative analysis can be performed using mathematical modelling. In practice, the feasibility of such a quantitative analysis will depend on the time available for decision-making and data collection concerning the problem. Key words: Mathematical models, plant health, predictive models.
Mindfulness-Based Relapse Prevention Program for Alcoholism: A Case-Control Study

Objective: To test the efficacy mindfulness-based relapse prevention program (MBRP) in alcohol dependent patients. Methods: The experimental study was carried out from June 2012 to March 2013. The MBRP was conducted in five 90-minute sessions and one half- day session, following Buddhist concepts related to Sati development. The objectives of the program were to develop subject’s awareness and acceptance of feeling and thought without identification with them. The program focuses on mindfulness practice in daily life. Subjects volunteered to participate in the study. The control group was matched selected and received treatments as usual. The number of cases who stopped drinking, dropped out and relapsed within 16 weeks were analyzed with Survival Analysis. Results: There were 30 cases of alcohol dependent males equally entering to the study and the control groups. The median time to relapse of the study group was significantly longer than that of the control group (8 wks vs 2 wks, p=.04). At the end of the study, 8 cases in the study group compared with 3 cases in the control group were abstinent. No subject in the study group was readmitted while 8 cases in the control group did so. Conclusion: The MBRP can help to prolong abstinent period and probably improve other clinical outcomes of the alcohol dependent subjects. However longer-term study in a larger sample should be carried out. Key words: Alcohol, mindfulness, relapse prevention
High-order harmonic generation at 4 MHz as a light source for time-of-flight photoemission spectroscopy

We demonstrate high-order harmonic generation (HHG) at 4 MHz driven by a long-cavity femtosecond laser oscillator. The laser output is used directly in a tight focusing geometry, where the harmonics are generated from a gas jet with high backing pressure. The harmonic light source is applied to time-of-flight photoemission spectroscopy, and the characteristic electronic structure of Cu(111) is measured. Our results suggest a straightforward design of high-order harmonic generation at megahertz repetition rate and pave the way for applications in electron spectroscopy and microscopy.
Alternative Silver Stain Detection protocol for the GenePrintÂ® STR System Applied to Mestizo Population From Jalisco (West of Mexico)

1 *, Salazar-Flores J 1 , Munoz-Valle JF 2 , Torres-Jasso JH 1 and Paez-Riberos LA 3 Abstract A population sample of 163 unrelated individuals from the Mexican state of Jalisco (West of Mexico) was PCR- typed with the Geneprint® STR System including nine autosomal STRs (CSF1PO, TPOX, TH01, F13A01, FESFPS, vWA, D16S539, D7S820 and D13S317). For this purpose, we implemented an alternative protocol for STR silver stain detection, which provides some economical and technical benefits: 1) make easy the gel handling; 2) simplify the process avoiding the use of some -toxic- reagents; 3) require lesser timer and made-in-home solutions; 4) the original gels can be dried and stored for re-analysis, if necessary. The allele frequencies estimated were similar to a previous report from the same Mexican population, which allowed pooling STR genotype data for upgrade the forensic parameter estimates (n= 472). However, this is the first -and unique- population study in Mexico for F13A01 and FESFPS; thus, the sample size did not increased for these loci (n= 163). In the studied population, genotype distribution by locus and two-loci combination was in agreement with Hardy-Weinberg expectations for all nine STRs. For the STR system, the power of discrimination (PD) and exclusion (PE) were >99.999% and 99.9%, respectively.
Activation of Corticothalamic Layer 6 Cells Decreases Angular Tuning in Mouse Barrel Cortex

In the mouse whisker system, the contribution of L6 corticothalamic cells (L6 CT) to cortical and thalamic processing of the whisker deflection direction was investigated. A genetically defined population of L6 CT cells project to infragranular GABAergic interneurons that hyperpolarize neurons in somatosensory barrel cortex (BC). Optogenetic activation of these neurons switched BC to an adapted mode in which excitatory cells lost their angular tuning. In contrast, however, this was not the case with a general activation of inhibitory interneurons via optogenetic activation of Gad2-expressing cells. The decrease in angular tuning, when L6 CT cells were activated, was due to changes in cortical inhibition, and not inherited from changes in the thalamic output. Furthermore, L6 CT driven cortical inhibition, but not the general activation of GABAergic interneurons, abolished adaptation to whisker responses. In the present study, evidence is presented that a subpopulation of L6 CT activates a specific circuit of GABAergic interneurons that will predispose neocortex toward processing of tactile information requiring multiple whisker touches, such as in a texture discrimination task.
On the Economic Value of Alphas

In this paper, we examine the benefit of incorporating test assets with nonzero alphas into an optimal portfolio when the mean and covariance matrix of asset returns are estimated with errors. Under the normality assumption, we derive the distribution of out-of-sample return of a portfolio that is optimized based on sample mean and covariance matrix. We show that as long as the benchmarks are not ex ante efficient, this sample optimal portfolio will generate positive alpha relative to the benchmarks. However, due to estimation errors, we need a very long estimation window for the sample optimal portfolio to outperform the benchmarks. We further consider a strategy that optimally combines the risk-free asset, the sample optimal portfolio, and the sample optimal portfolio based on just the benchmarks. This combining strategy consistently outperforms the benchmarks, providing a reliable way to realize the economic value of nonzero alphas.