Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of Carbapenemase Genes among Carbapenem-Non-Susceptible Acinetobacter baumanii Blood Isolates in Indonesia: A Multicenter Study

Carbapenem non-susceptible Acinetobacter baumannii (CNSAB) is an important pathogen that causes nosocomial bacteremia among critically ill patients worldwide. The magnitude of antibiotic resistance of A. baumanii in Indonesia is expected to be significant; however, the data available are limited. The aim of this study was to analyze the genetic profiles of CNSAB isolates from patients with bacteremia in Indonesia. CNSAB isolates from blood cultures of bacteremia patients in 12 hospitals in Indonesia were included. The blood cultures were conducted using the BacT/Alert or BACTEC automated system. The CNSAB were identified with either Vitek 2 system or Phoenix platform followed by a confirmation test using a multiplex polymerase chain reaction (PCR) assay, targeting the specific gyrB gene. The carbapenemase genes were detected by multiplex PCR. In total, 110 CNSAB isolates were collected and were mostly resistant to nearly all antibiotic classes. The majority of CNSAB isolates were susceptible to tigecycline and trimethoprim-sulfamethoxazole (TMP-SMX), 45.5% and 38.2%, respectively. The blaOXA-51-like gene was identified in all CNSAB isolates. Out of the total, 83.6% of CNSAB isolates had blaOXA-23-like gene, 37.3% blaOXA-24-like gene, 4.5% blaNDM-1 gene, 0.9% blaIMP-1 gene, and 0.9% blaVIM gene. No blaOXA-48-like gene was identified. The blaOXA-23-like gene was the predominant gene in all except two hospitals. The presence of the blaOXA-24-like gene was associated with resistance to tigecycline, amikacin, TMP-SMX and cefoperazone-sulbactam, while blaOXA-23-like gene was associated with resistance to TMP-SMX and cefoperazone-sulbactam. In conclusion, the blaOXA-23-like gene was the predominant gene among CNSAB isolates throughout Indonesia. A continuous national surveillance system needs to be established to further monitor the genetic profiles of CNSAB in Indonesia.
Robust Estimation of Large Panels with Factor Structures

Abstract This article studies estimation of linear panel regression models with heterogeneous coefficients using a class of weighted least squares estimators, when both the regressors and the error possibly contain a common latent factor structure. Our theory is robust to the specification of such a factor structure because it does not require any information on the number of factors or estimation of the factor structure itself. Moreover, our theory is efficient, in certain circumstances, because it nests the GLS principle. We first show how our unfeasible weighted-estimator provides a bias-adjusted estimator with the conventional limiting distribution, for situations in which the OLS is affected by a first-order bias. The technical challenge resolved in the article consists of showing how these properties are preserved for the feasible weighted estimator in a double-asymptotics setting. Our theory is illustrated by extensive Monte Carlo experiments and an empirical application that investigates the link between capital accumulation and economic growth in an international setting. Supplementary materials for this article are available online.
Dual-Function Semaphorin 4D Released by Platelets: Suppression of Osteoblastogenesis and Promotion of Osteoclastogenesis

Effects of the antiosteoblastogenesis factor Semaphorin 4D (Sema4D), expressed by thrombin-activated platelets (TPs), on osteoblastogenesis, as well as osteoclastogenesis, were investigated in vitro. Intact platelets released both Sema4D and IGF-1. However, in response to stimulation with thrombin, platelets upregulated the release of Sema4D, but not IGF-1. Anti-Sema4D-neutralizing monoclonal antibody (mAb) upregulated TP-mediated osteoblastogenesis in MC3T3-E1 osteoblast precursors. MC3T3-E1 cells exposed to TPs induced phosphorylation of Akt and ERK further upregulated by the addition of anti-sema4D-mAb, suggesting the suppressive effects of TP-expressing Sema4D on osteoblastogenesis. On the other hand, TPs promoted RANKL-mediated osteoclastogenesis in the primary culture of bone-marrow-derived mononuclear cells (BMMCs). Among the known three receptors of Sema4D, including Plexin B1, Plexin B2 and CD72, little Plexin B2 was detected, and no Plexin B1 was detected, but a high level of CD72 mRNA was detected in RANKL-stimulated BMMCs by qPCR. Both anti-Sema4D-mAb and anti-CD72-mAb suppressed RANKL-induced osteoclast formation and bone resorptive activity, suggesting that Sema4D released by TPs promotes osteoclastogenesis via ligation to a CD72 receptor. This study demonstrated that Sema4D released by TPs suppresses osteogenic activity and promotes osteoclastogenesis, suggesting the novel property of platelets in bone-remodeling processes.
Systematic revision of the red algal genus Yonagunia (Halymeniaceae, Rhodophyta) from Taiwan, including the description of two new species

ABSTRACT Among the eight species of Yonagunia described in the Indo-Pacific region, five species have been reported from Taiwan. In this study, we re-examined additional herbarium specimens which were morphologically similar to the other Taiwanese species of Yonagunia. Two new species of Yonagunia (Y. robusta sp. nov. and Y. stipitata sp. nov.) were identified based on rbcL sequence analyses, and their vegetative and reproductive structures were documented in detail. Yonagunia robusta is the largest species (up to 13 cm high) found in Taiwan and superficially resembles a previously described species, Y. palmata from northern Taiwan, but the thallus size is much larger and the branches are coarser in Y. robusta. Young plants of Y. stipitata may be confused with Y. maillardii, a species widely distributed in the Indo-Pacific, but the thallus branches are much thinner and numerous reproductive branchlets are formed in clusters in fertile Y. stipitata. Yonagunia robusta is widely distributed from northern to south-eastern Taiwan, whereas Y. stipitata is restricted to Orchid Island, a remote small island off the south-east of Taiwan. The species diversity (seven out of 10 described species) of Yonagunia is high in Taiwan and it is speculated that some more cryptic species will be found from the Indo-Pacific by using a combination of DNA sequence data and morphological observations. HIGHLIGHTS Ten species of Yonagunia have been described from the Indo-Pacific. Seven out of 10 species of Yonagunia are found in Taiwan. Cryptic species of Yonagunia will be found in the Indo-Pacific.
COVID-19 Vaccine Hesitancy: The Role of Information Sources and Beliefs in Dutch Adults

COVID-19 vaccine hesitancy may be regarded as a new pandemic hindering the elimination of or coping with COVID-19. This study assessed reasons for COVID-19 vaccine hesitancy using the I-Change Model (ICM) by considering the role of informational and psychosocial factors. A cross-sectional online survey using a convenience sample was conducted among Dutch adults (n = 240). The questionnaire assessed information factors, predisposing factors, awareness factors, motivational factors, preparatory actions, and vaccination intention. Vaccine hesitant participants (n = 58, 24%) had lower levels of education, more often paid work, and tended to have a religion other than Catholicism. They used written media less often and tended to visit websites of public health organizations less often, but used messaging services like WhatsApp more frequently. All participants had neutral intentions towards checking information credibility. Vaccine hesitant respondents had less knowledge about vaccination, lower perceived severity of getting sick and dying of COVID-19, and reported fewer exposures to cues about the advantages of COVID-19 vaccination. They were less convinced of the emotional and rational advantages of COVID-19 vaccination and expressed more negative feelings about it. They also reported more negative social norms concerning COVID-19 vaccination, and lower self-efficacy to get vaccinated and to cope with potential side-effects. The regression model explained 58% of the variance in vaccination intention. The results suggest that strategies are needed to: 1. Reduce fake news and stimulate information checking to foster well-informed decision-making; 2. Target both rational and emotional consequences of COVID-19, in addition to strategies for optimizing levels of knowledge. Campaigns should acknowledge the perceptions of the emotional disadvantages and increase perceptions of emotional advantages of COVID-19 vaccinations, such as reducing feelings of regret, and increasing feelings of freedom and reassurance.
Molecular characterization and cultivation of edible wild mushrooms, Lentinus sajor-caju, L. squarrosulus and Pleurotus tuber-regium from Sri Lanka

Tropical wild edible mushrooms are nutritious, delicious and economically important fungal bioresources. In this study, two edible Lentinus species and one Pleurotus species were collected from Central and Western provinces of Sri Lanka. After the initial morphological identification, growth rates and culture characteristics were observed in four different culture media. Genomic DNA was extracted and PCR amplifications of fungal barcode, nuclear ribosomal internal transcribed spacers 1, 2 and 5.8S (ITS) region were carried out. Molecular phylogenetic analyses confirmed the identity of the isolates as Lentinus squarrosulus, L. tuber-regium and Pleurotus sajor-caju. The possibilities of cultivation of the species collected were investigated using rice and corn as the spawn media, while rubber and mango saw dust were used as the basal media. A commercial P. ostreatus strain was used as a positive control strain alongside all experiments. All three newly collected species showed the highest growth rates on Potato Dextrose Agar (PDA) and the highest mycelial density on corn spawn. Mycelia of all the isolates showed the highest growth rate in mango saw dust medium. Pleurotus tuber-regium, L. sajor-caju and L. squarrosulus produced fruit bodies 69, 88 and 49 days after spawning respectively. Highest mean yield for P. tuber-regium was observed in rubber saw dust (110.617 g ± 15.828), for L. sajor-caju in mango saw dust (13.978 g ± 3.656) and for L. squarrosulus in rubber saw dust (51.350 g ± 0). Based on the available information, this is the first successful cultivation of L. sajor-caju and P. tuber-regium strains collected from Sri Lanka.
Phenotypic and Histological Distribution Analysis Identify Mast Cell Heterogeneity in Non-Small Cell Lung Cancer

Simple Summary During the fight against tumor, some cells of the immune system such as cytotoxic lymphocytes eliminate tumoral cells while others such as tumor-associated macrophages favor tumor development. Mast cells (MCs) are multifaceted immune cells whose role in cancer is still poorly understood. Moreover, MCs are poorly characterized in the context of cancer and their presence in the tumor microenvironment has been reported to be either associated with good or bad prognosis. In this pilot study we characterized tumor-associated MCs (TAMCs) in lung cancer. We showed that TAMCs exhibited a typical phenotype and can be classified in two subsets according to alphaE integrin (CD103) expression. CD103+ TAMCs appeared more mature, more prone to interact with CD4+ T cells, and located closer to cancer cells than their CD103− counterpart. This study revealed that a high frequency of total TAMC correlated with better overall survival and progression free survival in patients and underlined MC heterogeneity in cancer. Abstract Mast cells (MCs) are multifaceted innate immune cells often present in the tumor microenvironment (TME). However, MCs have been only barely characterized in studies focusing on global immune infiltrate phenotyping. Consequently, their role in cancer is still poorly understood. Furthermore, their prognosis value is confusing since MCs have been associated with good and bad (or both) prognosis depending on the cancer type. In this pilot study performed on a surgical cohort of 48 patients with Non-Small Cell Lung Cancer (NSCLC), we characterized MC population within the TME and in matching non-lesional lung areas, by multicolor flow cytometry and confocal microscopy. Our results showed that tumor-associated MCs (TAMCs) harbor a distinct phenotype as compared with MCs present in non-lesional counterpart of the lung. Moreover, we found two TAMCs subsets based on the expression of CD103 (also named alphaE integrin). CD103+ TAMCs appeared more mature, more prone to interact with CD4+ T cells, and located closer to cancer cells than their CD103− counterpart. In spite of these characteristics, we did not observe a prognosis advantage of a high frequency of CD103+ TAMCs, while a high frequency of total TAMC correlated with better overall survival and progression free survival. Together, this study reveals that TAMCs constitute a heterogeneous population and indicates that MC subsets should be considered for patients’ stratification and management in future research.
Product Optimization, Storage Quality and Sensory Acceptance of Low Calorie Beverage Developed from Bitter Gourd and Kiwifruit

Bitter gourd (Momordica charantia L.) fruit is good source of many nutraceutical compounds and possess antioxidant, anti-diabetic and hypoglycaemic activities. However, its utilization in the preparation of beverages is limited due to its bitter after taste. Therefore, to realize the functional and therapeutic benefits of bitter gourd, an attempt was made to optimize nutritious and low caloriebitter gourd based beverage by blending with kiwifruit (Actinidia deliciosa), a store house of bioactive compounds and substituting sugar with stevioside (steviol glycoside). The standard (sugar sweetened) bitter gourd (BG)-kiwifruit (K) blended beverage was developed by utilizing 30% fruit part of BG:K blended juice (80: 20) with 40B TSS and 1.3% acidity. Further, to develop the low calorie beverage, sucrose (table sugar) was replaced with 25, 50, 75 and 100% equi-sweetness level of stevioside (steviol glycoside). Results revealed that 75% substitution of sucrose with stevioside resulted in shelf stable beverage with identical taste, good antioxidant potential (68.80%) and strong antimicrobial activity (26 mm ZOI) with reduced calorie values (28.5 Kcal/100g) compared to the sugar sweetened control sample (150.60 Kcal/100g). Hence, the developed beverage can HIGHLIGHTS • Low calorie Bitter gourd-Kiwifruit beverage has good antioxidant potential and sensory acceptability. • Product optimization showed about 80% reduction in calorie value. • Optimized beverage showed good storage stability at ambient conditions for a period of six months. Sharma, R. ; et al. 2 Brazilian Archives of Biology and Technology. Vol.65: e22210371, 2022 www.scielo. br/babt be commercialized as low calorie beverage with additional health benefits of natural compounds of bitter gourd and kiwifruit with highest bioactivity.
Student evaluations of using virtual reality to investigate natural hazard field sites

ABSTRACT At a time when traditional fieldwork is coming under pressure, be it from shrinking budgets, reducing carbon footprints, increased concerns for personal safety or the desire to make field skills accessible to all, how do we ensure that the key skills of observation, data collection and landscape analysis can still be developed in our students? This paper evaluates the experiences of students using immersive virtual reality (VR) to interrogate highly accurate georeferenced landscape models, made from data collected by Unmanned Aerial Vehicles, through the medium of Q methodology. It finds that there appears to be an association between prior engagement and expertise with IT and gaming technologies, such that those who declare some degree of prowess engage with and embrace the opportunities of using VR. This suggests that to allow more students to adopt positive approaches to learning in this manner, educators need to worry less about ever complex and realistic models, and invest more into positive prior experiences of using technology. Moreover, an important voice in the narrative around the physical nature of “being in the field” and social interaction with peers and tutors questions an approach that is still a relatively solitary experience.
Engaging busy teachers of young learners in in-service English training

Highly qualified and competent teachers are the key for outstanding education systems. Teachers, however, are too busy with administrative work. Accordingly conducting engaging in-service training for them is a relief, as well as a way to improve their teaching skills. The aim of this research is to report the in-service English training in a bilingual school in Yogyakarta Special Province, Indonesia, which the outcome is to improve the English skills of the teachers as a means of teaching (EMI � English as a Medium of Instruction). Questionnaires, interviews, and written reflections were the techniques of collecting the data. The result of the training shows that through some light hands-on activities, the teachers� motivation and engagement improved. This improvement resulted in the increase in using classroom language instructions.
Self-Excited Blade Vibration Experimentally Investigated in Transonic Compressors: Rotating Instabilities and Flutter

This paper investigates the vibrations that occurred on the blisk rotor of a 1.5-stage transonic research compressor designed for aerodynamic performance validation and tested in various configurations at Technische Universitat Darmstadt.During the experimental test campaign self-excited blade vibrations were found near the aerodynamic stability limit of the compressor. The vibration was identified as flutter of the first torsion mode and occurred at design speed as well as in the part-speed region. Numerical investigations of the flutter event at design speed confirmed negative aerodynamic damping for the first torsion mode, but showed a strong dependency of aerodynamic damping on blade tip clearance.In order to experimentally validate the relation between blade tip clearance and aerodynamic damping, the compressor tests were repeated with enlarged blade tip clearance for which stability of the torsion mode was predicted.During this second experimental campaign, strong vibrations of a different mode limited compressor operation. An investigation of this second type of vibration found rotating instabilities to be the source of the vibration. The rotating instabilities first occur as an aerodynamic phenomenon and then develop into self-excited vibration of critical amplitude.In a third experimental campaign, the same compressor was tested with reference blade tip clearance and a non-axisymmetric casing treatment. Performance evaluation of this configuration repeatedly showed a significant gain in operating range and pressure ratio. The gain in operating range means that the casing treatment successfully suppresses the previously encountered flutter onset. The aeroelastic potential of the non-axisymmetric casing treatment is validated by means of the unsteady compressor data.By giving a description of all of above configurations and the corresponding vibratory behavior, this paper contains a comprehensive summary of the different types of blade vibration encountered with a single transonic compressor rotor. By investigating the mechanisms behind the vibrations, this paper contributes to the understanding of flow induced blade vibration. It also gives evidence to the dominant role of the tip clearance vortex in the fluid-structure-interaction of tip critical transonic compressors. The aeroelastic evaluation of the non-axisymmetric casing treatment is beneficial for the design of next generation casing treatments for vibration control.Copyright © 2015 by ASME
Toward a Global Model for Soil Inorganic Phosphorus Dynamics: Dependence of Exchange Kinetics and Soil Bioavailability on Soil Physicochemical Properties

The representation of phosphorus (P) cycling in global land models remains quite simplistic, particularly on soil inorganic phosphorus. For example, sorption and desorption remain unresolved and their dependence on soil physical and chemical properties is ignored. Empirical parameter values are usually based on expert knowledge or data from few sites with debatable global representativeness in most global land models. To overcome these issues, we compiled from data of inorganic soil P fractions and calculated the fraction of added P remaining in soil solution over time of 147 soil samples to optimize three parameters in a model of soil inorganic P dynamics. The calibrated model performed well (r2 > 0.7 for 122 soil samples). Model parameters vary by several orders of magnitude, and correlate with soil P fractions of different inorganic pools, soil organic carbon and oxalate extractable metal oxide concentrations among the soil samples. The modeled bioavailability of soil P depends on, not only, the desorption rates of labile and sorbed pool, inorganic phosphorus fractions, the slope of P sorbed against solution P concentration, but also on the ability of biological uptake to deplete solution P concentration and the time scale. The model together with the empirical relationships of model parameters on soil properties can be used to quantify bioavailability of soil inorganic P on various timescale especially when coupled within global land models.
Towards Accurate Point-of-Care Tests for Tuberculosis in Children

In childhood tuberculosis (TB), with an estimated 69% of missed cases in children under 5 years of age, the case detection gap is larger than in other age groups, mainly due to its paucibacillary nature and children’s difficulties in delivering sputum specimens. Accurate and accessible point-of-care tests (POCTs) are needed to detect TB disease in children and, in turn, reduce TB-related morbidity and mortality in this vulnerable population. In recent years, several POCTs for TB have been developed. These include new tools to improve the detection of TB in respiratory and gastric samples, such as molecular detection of Mycobacterium tuberculosis using loop-mediated isothermal amplification (LAMP) and portable polymerase chain reaction (PCR)-based GeneXpert. In addition, the urine-based detection of lipoarabinomannan (LAM), as well as imaging modalities through point-of-care ultrasonography (POCUS), are currently the POCTs in use. Further to this, artificial intelligence-based interpretation of ultrasound imaging and radiography is now integrated into computer-aided detection products. In the future, portable radiography may become more widely available, and robotics-supported ultrasound imaging is currently being trialed. Finally, novel blood-based tests evaluating the immune response using “omic-“techniques are underway. This approach, including transcriptomics, metabolomic, proteomics, lipidomics and genomics, is still distant from being translated into POCT formats, but the digital development may rapidly enhance innovation in this field. Despite these significant advances, TB-POCT development and implementation remains challenged by the lack of standard ways to access non-sputum-based samples, the need to differentiate TB infection from disease and to gain acceptance for novel testing strategies specific to the conditions and settings of use.