Miracle-dz/UniFAR-FTUs huggingface dataset:
Seed germination thermal niche differs among nine populations of an annual plant: A modeling approach

Abstract Germination timing is an important determinant of survival and niche breadth of plants. The annual plant Nigella sativa occurs in diverse environments along a steep temperature gradient and thus is a suitable model for the study of germination behavior in response to temperature. We used a modeling approach to compare the germination thermal niche of seeds of nine populations of N. sativa produced in a common garden. Germination time courses were obtained by a newly developed process‐based model, and thermal niche was visualized by plotting germination breadth as a function of after‐ripening time. Seeds were sampled five times: immature (2 weeks before maturity), mature, and afterripened for 1, 2, and 5 months. Immature and mature seeds had a greater depth of dormancy than afterripened seeds, as estimated by lower values of high‐limit temperatures (T h). Afterripening increased germination percentage, synchrony, and thermal niche breadth of all nine populations. The highest asynchrony was for immature and mature seeds, and afterripening enhanced synchrony. Based on the new graphical method, N. sativa has Type 1 nondeep physiological dormancy, and thus, the germination niche is narrow at seed maturity, leading to a delayed germination strategy that is highly dependent on thermal time accumulated during afterripening. Our findings show that there is considerable variation in the germination thermal niche among populations. Temperature regimes in the natural habitats of N. sativa have played a significant role in shaping variation in thermal niche breadth for seed germination of this annual species. The models used in our study precisely predict germination behavior and thermal niche under different environmental conditions. The germination synchrony model also can estimate germination pattern and degree of dormancy during the year, suggesting a useful method for quantification of germination strategies.
Direct Identification of Urinary Tract Pathogens by MALDI-TOF/TOF Analysis and De Novo Peptide Sequencing

For mass spectrometry-based diagnostics of microorganisms, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently routinely used to identify urinary tract pathogens. However, it requires a lengthy culture step for accurate pathogen identification, and is limited by a relatively small number of available species in peptide spectral libraries (≤3329). Here, we propose a method for pathogen identification that overcomes the above limitations, and utilizes the MALDI-TOF/TOF MS instrument. Tandem mass spectra of the analyzed peptides were obtained by chemically activated fragmentation, which allowed mass spectrometry analysis in negative and positive ion modes. Peptide sequences were elucidated de novo, and aligned with the non-redundant National Center for Biotechnology Information Reference Sequence Database (NCBInr). For data analysis, we developed a custom program package that predicted peptide sequences from the negative and positive MS/MS spectra. The main advantage of this method over a conventional MALDI-TOF MS peptide analysis is identification in less than 24 h without a cultivation step. Compared to the limited identification with peptide spectra libraries, the NCBI database derived from genome sequencing currently contains 20,917 bacterial species, and is constantly expanding. This paper presents an accurate method that is used to identify pathogens grown on agar plates, and those isolated directly from urine samples, with high accuracy.
Metabolic and Developmental Changes in Germination Process of Mung Bean (Vigna radiata (L.) R. Wilczek) Sprouts under Different Water Spraying Interval and Duration

Mung bean is one of the world’s most important legume crops and is a major protein source, particularly in developing countries. Various polyphenolic compounds and nutrients accumulate in mung bean sprouts during germination. Mung bean sprouts are consumed globally as an excellent food source of bioactive phenolic compounds. The contents of phenols and flavonoids and antioxidant activity were monitored for four days after germination under four different spraying conditions using three mung bean cultivars. On the third day after germination, the sprout extract showed the highest antioxidant capacity. The length and thickness of hypocotyl of mung bean sprouts appeared to be the most suitable for consumption on the third day after germination. Using high-performance liquid chromatography analysis, eight phytochemicals were identified, and neochlorogenic acid was identified for the first time in mung bean sprouts. End products (neochlorogenic acid, chlorogenic acid, vitexin, and isovitexin) showed certain trends in their contents for four days, while intermediates (caffeic acid, catechin, syringic acid, and p-coumaric acid) were highly responsive to watering condition and cultivars. Watering interval significantly affected the length of root and lateral root development. Both cultivars and watering conditions and/or their interaction significantly affected the biochemical and physical traits of mung bean sprouts. The results suggest that watering conditions need to be considered as an important factor to improve food quality of mung bean sprouts. Our phenotypic and metabolic profiling would provide potential information for production of mung bean sprouts that fit consumers’ preferences.
Description of the larva of Vestalis melania (Selys, 1873) (Odonata: Calopterygidae) identified through DNA barcoding

The larva of Vestalis melania is described and illustrated for the first time, based on specimens collected from Malaybalay, Bukidnon, Philippines. The identity of the larva was confirmed by matching its mitochondrial COI sequence with the adult. The larva can be distinguished by the shape of the prementum and its median cleft, lateral gills, and posterolateral abdominal spines. Comparison with other known larvae in the genus is also provided. The significance of using DNA barcoding for identifying larvae of Philippine Odonata is emphasized.
Researching property development in "interesting times"

As part of a wider study this paper will examine the impact of the economic downturn on a research project on property developers and discuss ways in which its focus and the methodology employed have necessarily changed. Research projects seek, at least, to develop overarching understandings of situations, if not an abstract generalised theory. This requires a degree of stability which allows similarities to be identified and comparisons to be made. The impact of the economic crisis has invalidated this assumption. However, in reality, property development operates against a background of changing economic, political and social conditions and it has long been acknowledged that the development cycle is signified by an alternating cycle of booms and slumps. These continuous changing circumstances were not factored into the first stage of this research which comprised a series of semi-structured interviews with independent trader developers. It was established that the lengthy nature of development allows a degree of flexibility to occur during implementation, thus, development projects are subject to varying levels of modification during the process. Alterations to the original development proposal are often made in reaction to changing market conditions to maximise returns. However, during the process of the research the UK property market collapsed. Second stage interviews show that speculative developments have all but stopped and funding for pre-lets and pre-sales has become significantly more difficult to come by. Interviewees now recall past experiences of recessions. This step change could be regarded as invalidating the research. The methodological and theoretical implications of this will be discussed, concluding that research has been enriched by this collapse revealing more correctly the nature of the field under view.
Broadcast News Transcription Baseline System using the NEMLAR database

This paper describes one of the first uses of the NEMLAR Arabic Broadcast News Speech Corpus (BNSC) for the creation of an automatic speech recognizer (ASR) for Arabic Broadcast News (BN). Different parameterization settings, types of acoustic models, various language models and testing schemes are presented for the creation of a baseline system for Modern Standard Arabic using the NEMLAR BNSC database. To port this system to dialects, a certain amount of dialectal data is required. Due to the absence of such resources and the use of other languages in dialectal speech, techniques for the creation of cross-lingual models using the baseline system are investigated. Certain techniques that have given promising results in previous experiments are proposed. These techniques, which would be helpful in developing a cross-dialectal speech recognition system, have been, due to the use of Maghrebian/Levantine dialects which make use of French, experimented in a cross-lingual Arabic-French frame. Although a lot of work remains to be accomplished, the current results are very encouraging.
Thyroid Cancer in Patients with Metabolic Syndrome or Its Components: A Nationwide Population-Based Cohort Study

Simple Summary The rapidly increasing coincidence of thyroid cancer and metabolic syndrome (MS) in recent decades suggests an association between the two disorders. To investigate this association, we conducted a nationwide study of a large-scale patient cohort. Between 2009 and 2011, data were collected by the Korean National Health Insurance Service for 4,658,473 persons aged 40–70 years without thyroid cancer. The incidence of thyroid cancer per 10,000 person-years in individuals with MS was significantly higher in men (6.2, p < 0.001) and women (21.3, p < 0.001) compared to those without MS. Additionally, the risk of thyroid cancer increased significantly with an increasing number of MS components even in individuals with only one or two MS components. MS and its components were significantly associated with increased risk of developing thyroid cancer. Abstract The rapidly increasing coincidence of thyroid cancer and metabolic syndrome (MS) in recent decades suggests an association between the two disorders. To investigate this association, we conducted a nationwide study of a large-scale patient cohort. Between 2009 and 2011, data were collected by the Korean National Health Insurance Service for 4,658,473 persons aged 40–70 years without thyroid cancer. During the six-year follow-up period, participants were monitored for the development of thyroid cancer. The relative risks and incidences of thyroid cancer were calculated using multivariate Cox proportional hazards regression analyses after adjusting for age and body mass index. The risk of thyroid cancer was significantly elevated in men and women with MS or MS components, except for hyperglycaemia (p = 0.723) or hypertriglyceridemia (p = 0.211) in men. The incidence of thyroid cancer per 10,000 person-years in individuals with MS was significantly higher in men (6.2, p < 0.001) and women (21.3, p < 0.001) compared to those without MS. Additionally, the risk of thyroid cancer increased significantly with an increasing number of MS components even in individuals with only one or two MS components. MS and its components were significantly associated with increased risk of developing thyroid cancer.
Does D2D Communication Always Benefit Physical-Layer Security?

Device-to-device (D2D) communication is able to enhance the spectrum efficiency and coverage of wireless networks but its transmission secrecy is vulnerable since D2D terminals are usually resource/power constrained. Various existing endeavors propose physical-layer security (PLS) means to protect D2D transmissions, under the default prerequisite that D2D transmissions always improve the secrecy performance. In this article, we show that this assumption/conclusion is invalid. We investigate a so-called cellular transmission mode assisted by the base station (cellular mode) and compare its secrecy performance with that of the D2D direct transmission (D2D mode). In both modes, subject to the secrecy outage probability constraints, we optimize the transceiver parameters, such as the signal power, secrecy rates, and transmission thresholds, to maximize the secrecy throughputs. All of the optimal solutions are obtained by closed-form expressions in both modes. Numerical results show that neither of the two transmission modes is always the better but highly depends on the system parameters, such as the locations of nodes, transmit power, and secrecy requirements, and consequently provides the answer that D2D communication is not always beneficial for PLS. This immediately suggests that an adaptive switching transmission mode could achieve an enhanced secrecy performance, which is also validated by simulations.
Establishment of production process and assurance method for alternating phase-shift masks

Alternating phase shift masks (altPSMs) are effective in reducing MEF. However, altPSMs have been used in device development, not in production, because phase-defect assurance has not been sufficient. An assurance method for 180- and 150-nm rule altPSMs was established by the use of both MD-2000 and KLA/STARlight. We have started production of defect-free altPSMs with quartz etched shifters and single trench structures by a two-step quartz etching process, which has an advantage of low phase-defect density.
Upper gastrointestinal bleeding: Do emergency endoscopic evaluations affect clinical outcomes?

Background: We aimed to reveal the effect of time from admission to endoscopy on clinical outcomes such as mortality, rebleeding, and prolonged hospitalization among patients with acute upper gastrointestinal bleeding. Methods: Patients aged ≥18 years with acute upper gastrointestinal bleeding were enrolled in the study. Those who had variceal bleeding during endoscopy, those whose hospital stay was shorter than 24 hours, those who did not undergo endoscopy, and those who underwent endoscopy after 24 hours were excluded from the study. Clinical findings, routine laboratory test results, and imaging findings of the patients were retrospectively reviewed through the hospital’s records system. Result: A total of 252 patients were enrolled in the study. At admission, 30.2% (76) of patients were at clinically high risk of death or rebleeding, 71.8% had melena, and 51.2% had hematemesis. While 72 (28.6%) of the patients had high-risk endoscopic stigmata, 89 (35.3%) had low-risk endoscopic stigmata. The median hospital stay was 6 (1-91) days. In-hospital mortality occurred in 8 (3.2%) cases, rebleeding developed in 16 (6.3%) cases, endoscopic intervention was required in 103 (40.9%) cases, and prolonged hospital stay was required in 43 (17.1%) cases. High-risk endoscopic stigmata were identified in 63 (34.1%) cases in the urgent group and in 9 (13.4%) in the early group (p=0.001). Endoscopic intervention was required in 47.0% cases in the urgent group, while the incidence was 23.9% in the early group (p=0.001). Conclusion: While no significant difference was found between the urgent and early groups in terms of mortality and re-bleeding, the need for endoscopic intervention and the incidence of high-risk endoscopic stigmata were found to be significantly higher in the urgent group.
ICN With DHT Support in Mobile Networks

Information-Centric Network (ICN) architectures, such as Named Data Networking (NDN), can improve content delivery on the Internet by deploying in-network caching techniques. Replacing the entire established Internet with a novel architecture is a non-trivial task, which is why this work develops a layered network architecture consisting of several smaller NDN-based mobile networks (resp., domains), interconnected using a Distributed Hash Table (DHT)-based network running as an overlay on top of existing Internet infrastructures. Using simulations, we model real-world network characteristics to evaluate the proposed architecture’s performance successfully.
Temperature Gradient Impact on Heat Exchanger Leaks Using CFD Analysis

– Heat exchanger leaks are common failures in gas and oil industry. However, the root causes of failure are not always obvious to identify. Therefore, utilizing advanced analysis tools such as computational fluid dynamics and finite element analysis are vital to better understand the problem. Here, we discuss a real case of a heat exchanger facing repeated leaks in an oil and gas industry. Detailed computational fluid dynamics analysis is used to determine the impact of temperature gradient on displacement of the heater flanges and gaskets. The simulated conditions include 5 steady-state and transient operating conditions. The analysis results show that thermal expansion cause loss of bolt load and further reduces gasket contact pressure. Maximum gasket scuffing due to differential radial thermal expansion could result in gasket damage over repeated thermal cycles. This finding is the most likely root cause of the repeated heater leaks. The results discuss additional potential root causes of the leaks mainly related to gasket damage due to thermal expansion behavior. The results of this work will be used for future work utilizing finite element analysis tools.
The Use of Virtual Environments and Simulation in Teacher Training

This study examines the scientific studies on the use of virtual environments and simulation programs in teacher training programs. Firstly, a search was made in the Web of Science database using the keywords simSchool and TeachLive. Four of the studies obtained as a result of the screening were excluded for various reasons (such as duplicate or off-topic publication) and the study was conducted with 22 scientific publications. The research results showed that virtual environments and simulations, which are widely and effectively used in many disciplines, also have a crucial potential in teaching and training. Most of the studies subject to analysis suggested that the use of virtual environments and simulation in education has positive effects such as self-confidence, time management, and classroom management. The research findings were discussed within the framework of the relevant literature, and suggestions were made.
Review on Nanomaterials and Nano-Scaled Systems for Topical and Systemic Delivery of Antifungal Drugs

Abstract Fungal infections are human infections that topically affect the skin, mucous membranes, or more serious, invasive, and systemic diseases of the internal organs. The design and advancement of the formulation and approach of administration for therapeutic agents depend on many variables. The correlation between the formulations, mode of administration, pharmacokinetics, toxicity and clinical indication must be thoroughly studied for the successful evolution of suitable drug delivery systems. There are several NP formulations that serve as good delivery approaches for antifungal drugs. This paper covers various groups of nanoparticles utilized in antifungal drug delivery, such as phospholipid-based vesicles (nanovesicles), non-phospholipid vesicles, polymeric nanoparticles, inorganic nanoparticles and dendrimers, whereby their advantages and drawbacks are emphasized. Many in vitro or cell culture studies with NP formulations achieve an adequate high drug-loading capacity; they do not reach the clinically significant concentrations anticipated for in vivo studies. Because of this, the transfer of these nano-formulations from the laboratory to the clinic could be aided by focusing studies on overcoming problems related to nanoparticle stability, drug loading, and high production and standardization costs.
Bioinformatics-Guided Identification of Ethyl Acetate Extract of Citri Reticulatae Pericarpium as a Functional Food Ingredient with Anti-Inflammatory Potential

Citri Reticulatae Pericarpium (CRP) is one of the most commonly used food supplements and folk medicines worldwide, and possesses cardiovascular, digestive, and respiratory protective effects partially through its antioxidant and anti-inflammatory functions. The unique aromatic flavor and mild side effects make CRP a promising candidate for the development of anti-inflammatory functional food. However, recent studies show that the crude alcoholic extract and some isolated compounds of CRP show compromised anti-inflammatory activity, which became the main factor hindering its further development. To identify the bioactive compounds with anti-inflammatory potential, and improve the anti-inflammatory effects of the extract, a bioinformatics-guided extraction protocol was employed in this study. The potential bioactive candidates were identified by combing network pharmacology analysis, molecular docking, principal components analysis, k-means clustering, and in vitro testing of reference compounds. Our results demonstrated that 66 compounds in CRP could be grouped into four clusters according to their docking score profile against 24 receptors, while the cluster containing flavonoids and phenols might possess a more promising anti-inflammatory function. In addition, in vitro anti-inflammatory tests of the seven reference compounds demonstrated that hesperitin, naringenin, and gardenin B, which were grouped into a cluster containing flavonoids and phenols, significantly decreased LPS-induced NO, TNF-α, and IL-6 production of macrophages. While the compounds outside of that cluster, such as neohesperidin, naringin, hesperidin, and sinensetin showed little effect on alleviating LPS-induced NO and proinflammatory cytokine production. Based on the chemical properties of selected compounds, ethyl acetate (EtOAc) was selected as the solvent for extraction, because of its promising solubility of flavonoids and phenols. Furthermore, the ethanol alcoholic extract was used as a reference. The chemical profiling of EtOAc and crude alcoholic extract by HPLC/MS/MS also demonstrated the decreased abundance of flavonoid glycosides in EtOAc extract but increased abundance of phenols, phenolic acid, and aglycones. In accordance with the prediction, the EtOAc extract of CRP, but not the crude alcoholic extract, significantly decreased the NO, IL-6, and TNF-α production. Taken together, the results suggested selective extraction of phenols and flavonoids rich extract was able to increase the anti-inflammatory potential of CRP partially because of the synergistic effects between flavonoids, phenols, and enriched polymethoxyflavones. Our study might pave the road for the development of ethyl acetate extract of CRP as a novel functional food with anti-inflammatory function.