Miracle-dz/UniFAR-FTUs huggingface dataset:
Exports and Employment in Indonesia: The Decline in Labor-Intensive Manufacturing and the Rise of Services

Employment generation has been a challenge in Indonesia since the Asian financial crisis, especially in labor-intensive manufacturing. Drawing on work by James and Fujita (2000), this paper examines the impact of exports on jobs, based on an analysis of input–output tables over the period 1995–2005. It finds that fewer jobs were created through exports in manufacturing industries in 2005 than before the crisis, because of slower growth in manufacturing exports and a shift away from light industry. The slowdown is potentially costly due to the endemic elastic supply of unskilled labor. However, there was an increase in jobs in the services sector, partly because of indirect connections with the main export industries. This could be enhanced through greater domestic and international competition in services. The main constraints to job creation through exports appear on the supply side, especially those related to poor infrastructure, an uncertain investment climate, and tight labor regulations.
The complete chloroplast genome sequence of wild cucumber (Cucumis sativus var. Hardwickii)

Abstract The complete chloroplast genome sequence of wild cucumber (Cucumis sativus var. hardwickii) was generated by de novo assembly with low-coverage whole-genome sequence data. The 155 277 bp genome containing a pair of inverted repeats (IRs) of 25 198 bp separated by a large single-copy region of 86 618 bp and a small single-copy region of 18 263 bp. The chloroplast genome contains 130 known genes, including 89 protein-coding genes, eight rRNA genes (four kinds), and 37 tRNA genes (30 kinds). Eighteen genes are duplicated in the inverted repeat regions, 16 genes contain one intron, two genes, and one ycf contain two introns. Phylogenomic analysis showed that C. sativus var. Hardwickii is closely related to C. sativus and C. hystrix.
A Fast Flowgraph Based Classification System for Packed and Polymorphic Malware on the Endhost

Identifying malicious software provides great benefit for distributed and networked systems. Traditional real-time malware detection has relied on using signatures and string matching. However, string signatures ineffectively deal with polymorphic malware variants. Control flow has been proposed as an alternative signature that can be identified across such variants. This paper proposes a novel classification system to detect polymorphic variants using flowgraphs. We propose using an existing heuristic flowgraph matching algorithm to estimate graph isomorphisms. Moreover, we can determine similarity between programs by identifying the underlying isomorphic flowgraphs. A high similarity between the query program and known malware identifies a variant. To demonstrate the effectiveness and efficiency of our flowgraph based classification, we compare it to alternate algorithms, and evaluate the system using real and synthetic malware. The evaluation shows our system accurately detects real malware, performs efficiently, and is scalable. These performance characteristics enable real-time use on an intermediary node such as an Email gateway, or on the end host.
Mood Instability and Irritability as Core Symptoms of Major Depression: An Exploration Using Rasch Analysis

Background Mood instability (MI) and irritability are related to depression but are not considered core symptoms. Instruments typically code clusters of symptoms that are used to define syndromic depression, but the place of MI and irritability has been under-investigated. Whether they are core symptoms can be examined using Rasch analysis. Method We used the UK Psychiatric Morbidity Survey 2000 data (n = 8,338) to determine whether the nine ICD/DSM symptoms, plus MI and irritability, constitute a valid depression scale. Rasch analysis was used, a method concerned with ensuring that items constitute a robust scale and tests whether the count of symptoms reflects an underlying interval-level measure. Two random samples of 500 were drawn, serving as calibration and validation samples. As part of the analysis, we examined whether the candidate symptoms were unidimensional, followed a Guttman pattern, were locally independent, invariant with respect to age and sex, and reliably distinguished different levels of depression severity. Results A subset of five symptoms (sad, no interest, sleep, cognition, suicidal ideas) together with mood instability and irritability satisfactorily fits the Rasch model. However, these seven symptoms do not separate clinically depressed persons from the rest of the population with adequate reliability (Cronbach α = 0.58; Person Separation Index = 0.35), but could serve as a basis for scale development. Likewise, the original nine DSM depression symptoms failed to achieve satisfactory reliability (Cronbach α = 0.67; Person Separation Index = 0.51). Limitations The time frame over which symptoms were experienced varied, and some required recall over the last year. Symptoms other than those examined here might also be core depression symptoms. Conclusion Mood instability and irritability are candidate core symptoms of the depressive syndrome and should be part of its clinical assessment.
Genetic Analysis Reveals the Essential Role of Nitrogen Phosphotransferase System Components in Sinorhizobium fredii CCBAU 45436 Symbioses with Soybean and Pigeonpea Plants

ABSTRACT The nitrogen phosphotransferase system (PTSNtr) consists of EINtr, NPr, and EIIANtr. The active phosphate moiety derived from phosphoenolpyruvate is transferred through EINtr and NPr to EIIANtr. Sinorhizobium fredii can establish a nitrogen-fixing symbiosis with the legume crops soybean (as determinate nodules) and pigeonpea (as indeterminate nodules). In this study, S. fredii strains with mutations in ptsP and ptsO (encoding EINtr and NPr, respectively) formed ineffective nodules on soybeans, while a strain with a ptsN mutation (encoding EIIANtr) was not defective in symbiosis with soybeans. Notable reductions in the numbers of bacteroids within each symbiosome and of poly-β-hydroxybutyrate granules in bacteroids were observed in nodules infected by the ptsP or ptsO mutant strains but not in those infected with the ptsN mutant strain. However, these defects of the ptsP and ptsO mutant strains were recovered in ptsP ptsN and ptsO ptsN double-mutant strains, implying a negative role of unphosphorylated EIIANtr in symbiosis. Moreover, the symbiotic defect of the ptsP mutant was also recovered by expressing EINtr with or without the GAF domain, indicating that the putative glutamine-sensing domain GAF is dispensable in symbiotic interactions. The critical role of PTSNtr in symbiosis was also observed when related PTSNtr mutant strains of S. fredii were inoculated on pigeonpea plants. Furthermore, nodule occupancy and carbon utilization tests suggested that multiple outputs could be derived from components of PTSNtr in addition to the negative role of unphosphorylated EIIANtr.
A comprehensive review of nanostructured materials by ultrasonic nanocrystal surface modification technique

Nanostructured materials (NMs) possess outstanding properties than conventional coarse-grained (CG) materials. Hence designing potentially cost-efficient and environmentally products made of NMs with better are on high demand. This paper gives a comprehensive review of the most recent progress in production, characterisation and fundamental understanding of NMs produced by ultrasonic nanocrystal surface modification (UNSM) technique. In this review, we demonstrate a detailed description of the literature on the subject as well as highlight challenges for the production of NMs. Recently, this technique has also been applied to thermal spray ceramic coatings and the newly obtained experimental results are also discussed.
Toolbox: Creating a systematic database of secretory pathway proteins uncovers new cargo for COPI

A third of yeast genes encode for proteins that function in the endomembrane system. However, the precise localization for many of these proteins is still uncertain. Here, we visualized a collection of ~500 N‐terminally, green fluorescent protein (GFP), tagged proteins of the yeast Saccharomyces cerevisiae. By co‐localizing them with 7 known markers of endomembrane compartments we determined the localization for over 200 of them. Using this approach, we create a systematic database of the various secretory compartments and identify several new residents. Focusing in, we now suggest that Lam5 resides in contact sites between the endoplasmic reticulum and the late Golgi. Additionally, analysis of interactions between the COPI coat and co‐localizing proteins from our screen identifies a subset of proteins that are COPI‐cargo. In summary, our approach defines the protein roster within each compartment enabling characterization of the physical and functional organization of the endomembrane system and its components.
Substrate Selectivity Check of the Ergothioneine Transporter

The candidate vitamin ergothioneine (ET) is a unique antioxidant. Expression of the ET transporter (ETT) (gene symbol SLC22A4) in distinct cells is thought to signal intracellular ET activity, since we have previously shown that the ETT is highly selective for ET. Unfortunately, some continue to hold the ETT as a relevant drug transporter, using the misleading functional name OCTN1, novel organic cation transporter. The present study was provoked by two recent reports in which new ETT substrates were declared. Astonishingly, the transport efficiencies (TEs) of ETT for saracatinib and some nucleoside drugs were as high as the TE for ET. Here we examined, based on regulated expression of ETT from human and rat in 293 cells and liquid chromatography-mass spectrometry quantification, the transport of several drugs. With the nucleosides cytarabine, gemcitabine, 2′-deoxycytidine, and 2′-deoxyadenosine, and the drugs saracatinib, ipratropium, metformin, and oxaliplatin, the uptake into cells expressing ETT was not increased over control cells. ETT-mediated uptake of gabapentin was detectable, but the TE was approximately 100-fold lower than the TE for ergothioneine (50–200 µl/min per milligram of protein). In conclusion, the ETT remains highly specific for its physiologic substrate ergothioneine. Our results contradict several reports on additional substrates. The ETT does not provide multiple substrate specificities, and it is not a transporter of cationic drugs. Only compounds that are related to ET in substructure—for example, gabapentin, carnitine, and TEA—can be transported, but with very low efficiency. Thus, ETT persists as a specific molecular indicator of ET activity.
Therapeutic drug monitoring for either oral or intravenous busulfan when combined with pre- and post-transplantation cyclophosphamide

Abstract Busulfan (Bu)/cyclophosphamide (Cy) is a standard conditioning platform for allogeneic transplantation. We developed a strategy separating the Cy into two pre/post-transplantation doses (PTCy), providing myeloablative conditioning and single-agent graft-versus-host disease (GVHD) prophylaxis. We investigated the impact of Bu route on treatment-related toxicity for 131 consecutive adult patients. Busulfan was administered in four daily divided doses either orally (n = 72) or intravenously (n = 59) with pharmacokinetics on the first-dose and as necessary on subsequent doses to achieve a target area-under-the-concentration-curve (AUC) of 800–1400 μmol*min/L per dose. BuCy/PTCy with pharmacokinetics is well-tolerated with low treatment-related toxicity. Hepatic veno-occlusive disease incidence was 6% with two fatal events. Bu administration route in the context of BuCy/PTCy did not statistically impact hepatotoxicity, GVHD, relapse, disease-free survival, or overall survival. The BuCy/PTCy platform has a low incidence of treatment-related toxicity, including hepatotoxicity, in hematologic malignancies when using pharmacokinetics for a target AUC of 800–1400 μmol*min/L, irrespective of Bu administration route.
T1/E1/J1 receiver in CMOS

Behavioural model, simulation and testing results of a mixed-signal short/long haul receiver suitable for the high speed T1/E1/J1 applications in CMOS are presented. The measured results demonstrate successful recovery of distorted incoming signals attenuated from 0-44 dB(max). The mixed-signal part of the receiver chip occupies area of 1.2 mm by 1.8 mm in CMOS 0.35 mum process and requires typically 120 mW of power at 3.3 V power supply. The operation of the receiver is supported by digital framer and local RAM is used for storing the unshielded twisted pair (UTP) cable models which can be easily reprogrammed.
Humeral quality and adrenal responsiveness in laying hens reared in standard and furnished cages

In order to find out whether furnished cages contribute to improving the welfare of laying hens, humerus quality and adrenal responsiveness were evaluated in laying hens reared in standard (S) and furnished cages (F). Four cage models were used: S5, a standard cage model with 5 hens per cage; S6, a standard cage model with 6 hens per cage; F7, a furnished cage model with 7 hens per cage (with a nest, dust-bathing box, two perches, and claw-shortening) and F15, a furnished cage model with 15 hens per cage (with a nest, dust-bathing box, two perches, and claw-shortening). At 72 weeks of age, maximal adrenal responsiveness was evaluated by measuring the changes in blood corticosterone level induced by the i.m. injection of 10 µg per hen of 1-24 ACTH (n = 15 hens per cage model). Hens (n = 15 to 23 hens per cage model) were slaughtered and the left and right humeri were used for measurement of weight, biomechanical characteristics in a flexion test, dry matter and ash percentage. Basal corticosterone levels did not differ significantly while the injection of ACTH produced a significant rise in corticosterone levels (P < 0.001) of similar amplitude for all cage mod- els. Humeri weights, biomechanical characteristics (elastic strain, bioyield point, stiffness and break- ing strength), dry weight and percentage of dry matter were not significantly different between cage models. The humeri ash percentage was significantly (P = 0.03) lower in birds from the S6 cage model (57.4%) than in birds from other cage models (S5: 59.0%; F7: 58.9%; F15: 59.7%). Adrenal responsiveness and major humeral characteristics were not significantly improved in furnished com- pared to standard cages in our experimental conditions. laying hen / furnished cages / exercise / bone / corticosterone / welfare
The mitochondrial genome of an endangered native Singidia tilapia, Oreochromis esculentus: genome organization and control region polymorphism

Abstract Singidia tilapia (Oreochromis esculentus) is a native Cichlid fish of important commercial value, distributed in Lake Victoria, East Africa. Due to its declining population levels in its natural habitat, this species has now been classified as a Critically Endangerd by the International Union for the Conservation of nature (IUCN). In the present study the complete nucleotide sequence of the mitochondrial genome (mtDNA) of O. esculentus was determined. In addition, polymorphism analysis based on the mtDNA’s control region sequence was investigated on two of its remaining populations of Yala and Borabu as well as a phylogenetic consideration using 16S rRNA mtDNA genes to explore its position and relationship within Cichlidae fish. The length of the complete mitogenome of O. esculentus is 16 622 bp, containing the same order and an identical number of genes and regions with the other reported Cichlid fishes, which consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative non-coding region. The phylogenetic analysis shows O. esculentus being clustered within the Oreochromini sub-tribe of the Cichlidae. The high genetic diversity and low genetic differentiation between the two populations indicated the need for conservation of both the refuge ecosystems and the fish species under study.
Sex Specific Association of Physical Activity on Proximal Femur BMD in 9 to 10 Year-Old Children

The results of physical activity (PA) intervention studies suggest that adaptation to mechanical loading at the femoral neck (FN) is weaker in girls than in boys. Less is known about gender differences associated with non-targeted PA levels at the FN or other clinically relevant regions of the proximal femur. Understanding sex-specific relationships between proximal femur sensitivity and mechanical loading during non-targeted PA is critical to planning appropriate public health interventions. We examined sex-specific associations between non-target PA and bone mineral density (BMD) of three sub-regions of the proximal femur in pre- and early-pubertal boys and girls. BMD at the FN, trochanter (TR) and intertrochanter (IT) regions, and lean mass of the whole body were assessed using dual-energy x-ray absorptiometry in 161 girls (age: 9.7±0.3 yrs) and 164 boys (age: 9.7±0.3 yrs). PA was measured using accelerometry. Multiple linear regression analyses (adjusted for body height, total lean mass and pubertal status) revealed that vigorous PA explained 3–5% of the variability in BMD at all three sub-regions in boys. In girls, vigorous PA explained 4% of the variability in IT BMD and 6% in TR BMD. PA did not contribute to the variance in FN BMD in girls. An additional 10 minutes per day of vigorous PA would be expected to result in a ∼1% higher FN, TR, and IT BMD in boys (p<0.05) and a ∼2% higher IT and TR BMD in girls. In conclusion, vigorous PA can be expected to contribute positively to bone health outcomes for boys and girls. However, the association of vigorous PA to sub-regions of the proximal femur varies by sex, such that girlś associations are heterogeneous and the lowest at the FN, but stronger at the TR and the IT, when compared to boys.
ISEA: Iterative Seed-Extension Algorithm for De Novo Assembly Using Paired-End Information and Insert Size Distribution

The purpose of de novo assembly is to report more contiguous, complete, and less error prone contigs. Thanks to the advent of the next generation sequencing (NGS) technologies, the cost of producing high depth reads is reduced greatly. However, due to the disadvantages of NGS, de novo assembly has to face the difficulties brought by repeat regions, error rate, and low sequencing coverage in some regions. Although many de novo algorithms have been proposed to solve these problems, the de novo assembly still remains a challenge. In this article, we developed an iterative seed-extension algorithm for de novo assembly, called ISEA. To avoid the negative impact induced by error rate, ISEA utilizes reads overlap and paired-end information to correct error reads before assemblying. During extending seeds in a De Bruijn graph, ISEA uses an elaborately designed score function based on paired-end information and the distribution of insert size to solve the repeat region problem. By employing the distribution of insert size, the score function can also reduce the influence of error reads. In scaffolding, ISEA adopts a relaxed strategy to join contigs that were terminated for low coverage during the extension. The performance of ISEA was compared with six previous popular assemblers on four real datasets. The experimental results demonstrate that ISEA can effectively obtain longer and more accurate scaffolds.
Drug resistance in patients with tuberculous pleural effusions

Purpose of review To summarize data regarding categories, detection methods, prevalence and patterns of drug resistance among patients with tuberculous pleural effusion (TPE) and to comment on the management of suspected drug-resistant TPE. Recent findings Pleural and pulmonary tuberculosis (TB) present similar patterns of drug resistance. Approximately 10% and 6–10% of pleural Mycobacterium tuberculosis isolates are resistant to at least one first-line anti-TB drug or at least isoniazid, respectively. The prevalence of multidrug-resistant-pleural and extensively drug-resistant-pleural TB is 1–3% and 0–1%, respectively. Summary Although guidelines suggest the empirical standard anti-TB regimen (i.e. 2 months of isoniazid, rifampicin, pyrazinamide and ethambutol followed by 4 months of isoniazid and rifampicin) for TPE treatment, the data regarding drug resistance among TPE patients are limited. The few studies examining the issue report a notable drug resistance. In suspected drug-resistant TPE, every effort is warranted to isolate M. tuberculosis to perform drug susceptibility testing and provide guided therapy. For this purpose, the use of cultures or molecular methods with pleural biopsies is superior to their use in pleural fluid. If still M. tuberculosis cannot be detected, prolonged administration of ethambutol with isoniazid and rifampicin during the continuation phase of treatment might be considered.
Design of Infusion Schemes for Neuroreceptor Imaging: Application to [11C]Flumazenil-PET Steady-State Study

This study aims at developing a simulation system that predicts the optimal study design for attaining tracer steady-state conditions in brain and blood rapidly. Tracer kinetics was determined from bolus studies and used to construct the system. Subsequently, the system was used to design inputs for bolus infusion (BI) or programmed infusion (PI) experiments. Steady-state quantitative measurements can be made with one short scan and venous blood samples. The GABAA receptor ligand [11C]Flumazenil (FMZ) was chosen for this purpose, as it lacks a suitable reference region. Methods. Five bolus [11C]FMZ-PET scans were conducted, based on which population-based PI and BI schemes were designed and tested in five additional healthy subjects. The design of a PI was assisted by an offline feedback controller. Results. The system could reproduce the measurements in blood and brain. With PI, [11C]FMZ steady state was attained within 40 min, which was 8 min earlier than the optimal BI (B/I ratio = 55 min). Conclusions. The system can design both BI and PI schemes to attain steady state rapidly. For example, subjects can be [11C]FMZ-PET scanned after 40 min of tracer infusion for 40 min with venous sampling and a straight-forward quantification. This simulation toolbox is available for other PET-tracers.
A Tree Regularized Classifier - Exploiting Hierarchical Structure Information in Feature Vector for Human Action Recognition

Bag of visual words is a popular model in human action recognition, but usually suffers from loss of spatial and temporal configuration information of local features, and large quantization error in its feature coding procedure. In this paper, to overcome the two deficiencies, we combine sparse coding with spatio-temporal pyramid for human action recognition, and regard this method as the baseline. More importantly, which is also the focus of this paper, we find that there is a hierarchical structure in feature vector constructed by the baseline method. To exploit the hierarchical structure information for better recognition accuracy, we propose a tree regularized classifier to convey the hierarchical structure information. The main contributions of this paper can be summarized as: first, we introduce a tree regularized classifier to encode the hierarchical structure information in feature vector for human action recognition. Second, we present an optimization algorithm to learn the parameters of the proposed classifier. Third, the performance of the proposed classifier is evaluated on YouTube, Hollywood2, and UCF50 datasets, the experimental results show that the proposed tree regularized classifier obtains better performance than SVM and other popular classifiers, and achieves promising results on the three datasets.