Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity

Animal venom systems have emerged as valuable models for investigating how novel polygenic phenotypes may arise from gene evolution by varying molecular mechanisms. However, a significant portion of venom genes produce alternative mRNA isoforms that have not been extensively characterized, hindering a comprehensive understanding of venom biology. In this study, we present a full-length isoform-level profiling workflow integrating multiple RNA sequencing technologies, allowing us to reconstruct a high-resolution transcriptome landscape of venom genes in the parasitoid wasp Pteromalus puparum. Our findings demonstrate that more than half of the venom genes generate multiple isoforms within the venom gland. Through mass spectrometry analysis, we confirm that alternative splicing contributes to the diversity of venom proteins, acting as a mechanism for expanding the venom repertoire. Notably, we identified seven venom genes that exhibit distinct isoform usages between the venom gland and other tissues. Furthermore, evolutionary analyses of venom serpin3 and orcokinin further reveal that the co-option of an ancient isoform and a newly evolved isoform, respectively, contributes to venom recruitment, providing valuable insights into the genetic mechanisms driving venom evolution in parasitoid wasps. Overall, our study presents a comprehensive investigation of venom genes at the isoform level, significantly advancing our understanding of alternative isoforms in venom diversity and evolution and setting the stage for further in-depth research on venoms.
Race and Area of Deprivation Index Predict Outcomes of Endoscopic Sinus Surgery for Chronic Sinusitis

Objective The purpose of this study is to characterize the presentation, outcomes, and barriers to care for White and non-White patients undergoing endoscopic sinus surgery (ESS). Background ESS is often successful in providing long-term relief for patients suffering from chronic rhinosinusitis (CRS). Literature that uses robust measures of socioeconomic status (SES) and barriers to care to assess ESS outcomes is limited. Methods A retrospective matched cohort study of patients who underwent ESS for CRS between 1/1/2015 and 6/1/2021 at a single tertiary care academic center was conducted. White and non-White patients were matched 1-to-1 by sex and age (± 5 years). SES was evaluated using the area of deprivation index (ADI). Results Of the 298 patients included in the study, 149 are White and 149 are non-White, 111 (37.2%) have CRS with nasal polyposis (CRSwNP), 141 (47.3%) had allergic rhinitis, 90 (30.2%) had asthma and 22 (7.4%) required revision ESS. Non-White patients were 3.62 times more likely to present with CRSwNP (95% confidence interval [CI] 2.2-5.96) and had 2.87 times increased odds for requiring revision ESS than age and sex-matched White patients (95% CI 1.090-7.545). The median ADI for non-White (6.00) patients was higher than for White patients (3.00) (P < .001) and 21.5% more non-White patients presented with Medicaid (P < .001). Conclusion Non-White patients undergoing ESS for CRS are more likely to present from areas with fewer resources and be underinsured. Using robust measures of SES, such as ADI, may allow for care to be tailored to patients with barriers to care.
Changes in stature of Portuguese women born between 1966 and 1982, according to educational level

Studies which document secular change in stature are almost exclusively based on males, while similar data on females is less common. In addition, secular trends in socioeconomic differences of height are seldomly reported. This study aims to document changes in mean stature in a sample of Portuguese women born between 1966 and 1982 (n = 30,629). For this study self-reported stature data was obtained from a large sample of women who delivered their children at the Dr. Alfredo da Costa Maternity Hospital, in Lisbon, between 1991 and 2004. Reported data on educational level was used as a proxy for socioeconomic status to assess changes in female stature in relation to their social class. Results show that female stature in the sample increases during the time period considered (mean stature: 160.8 cm in 1966 and 161.1 cm in 1982), but not consistently. In addition, women of higher educational level are systematically taller than their lower educational level counterparts (mean stature difference between highest and lowest educational level groups is 4.2 cm). Compared to males, mean stature increase in females was about 75% less. Although the time period considered is short, this study documents important socioeconomic differences in female stature and is the first to report stature changes over time in Portuguese women.
A condensed disaggregation model for incorporating parameter uncertainty into monthly reservoir simulations

A condensed version of the Valencia-Schaake disaggregation model is developed which describes the distribution of monthly streamflow sequences using a set of coupled univariate regression models rather than a multivariate time series formulation. The condensed model has fewer parameters and is convenient for generating flow sequences which incorporate the intrinsic variability of streamflows and the uncertainty in the parameters of the annual and monthly streamflow models. The impact of parameter uncertainty on derived relationships between reservoir capacity and reservoir performance statistics is illustrated using required reservoir capacity (calculated with the sequent peak algorithm), system reliability, and the average total shortfall. Modeled sequences describe flows in the Rappahannock River in Virginia and the Boise River in Idaho. For high-reliability systems the results show that streamflow generation procedures which ignore model parameter uncertainty can grossly underestimate reservoir system failure rates and the severity of likely shortages, even if based on a 50-year record.
Climate changes and their impacts on water resources in semiarid regions: a case study of the Wei River basin, China

Understanding the impacts of climate change and human activity on the hydrological processes in river basins is important for maintaining ecosystem integrity and sustaining local economic development. The objective of this study was to evaluate the impact of climate variability and human activity on mean annual flow in the Wei River, the largest tributary of the Yellow River. The nonparametric Mann–Kendall test and wavelet transform were applied to detect the variations of hydrometeorological variables in the semiarid Wei River basin in the northwestern China. The identifications were based on streamflow records from 1958 to 2008 at four hydrological stations as well as precipitation and potential evapotranspiration (PET) data from 21 climate stations. A simple method based on Budyko curve was used to evaluate potential impacts of climate change and human activities on mean annual flow. The results show that annual streamflow decreased because of the reduced precipitation and increased PET at most stations. Both annual and seasonal precipitation and PET demonstrated mixed trends of decreasing and increasing, although significant trends (P < 0.05) were consistently detected in spring and autumn at most stations. Significant periodicities of 0.5 and 1 year (P < 0.05) were examined in all the time series. The spectrum of streamflow at the Huaxian station shows insignificant annual cycle during 1971–1975, 1986–1993 and 1996–2008, which is probably resulted from human activities. Climate variability greatly affected water resources in the Beiluo River, whereas human activities (including soil and water conservation, irrigation, reservoirs construction, etc.) accounted more for the changes of streamflow in the area near the Huaxian station during different periods. The results from this article can be used as a reference for water resources planning and management in the semiarid Wei River basin. Copyright © 2012 John Wiley & Sons, Ltd.
Outcomes of Injection Laryngoplasty for Deep Interarytenoid Groove

Abstract Introduction Deep interarytenoid groove (DIG) may cause swallowing dysfunction in children; however, the management of DIG has not been established. Objective We evaluated the subjective and objective outcomes of interarytenoid augmentation with injection in children with DIG. Methods Consecutive children under 18 years of age who underwent injection laryngoplasty for DIG were reviewed. Data pertaining to demographics, past medical history, past surgical history, and results of pre and postoperative video fluoroscopic swallow study (VFSS) were obtained. The primary outcome measure was the presence of thin liquid aspiration or penetration on postoperative VFSS. The secondary outcome measure was caregiver-reported improvement of symptoms. Results Twenty-seven patients had VFSS before and after interarytenoid augmentation with injection (IA). Twenty (70%) had thin liquid penetration and 12 (44%) had thin liquid aspiration before the IA. Thin liquid aspiration resolved in 9 children (45%) and persisted in 11 (55%). Of the 12 children who had thin liquid aspiration prior to IA, 6 (50%) had resolution of thin liquid aspiration after IA. Conclusions Injection laryngoplasty is a safe tool to improve swallowing function in children with DIG. Further studies are needed to assess the long-term outcomes of IA and identify predictors of successful IA in children with DIG.
Ossäre Bedeutung von Mineral- und Heilwässern: Physiologie und epidemiologische Evidenz

Zusammenfassung Mineral- und Heilwässer zeichnen sich durch eine sortenspezifische Zusammensetzung aus, so dass sich die Wässer auch ausernährungsphysiologischer Sicht voneinander unterscheiden. Viele Mineral- und Heilwässer bilden eine quantitativ bedeutsame Quelle für gut bioverfügbares Calcium und Magnesium. Calciumreiche Wässer stellen somit eine günstige Alternative zum gut löslichen Calciumcitrat dar, wie es in der Leitlinie der Bone Health & Osteoporosis Foundation bei Achlorhydrie oder eingeschränkter Magensäureproduktion (z. B. Therapie mit Protonenpumpeninhibitoren) als Calciumquelle empfohlen wird. Calciumwässer senken den Serumspiegel an Parathormon ähnlich stark wie Calcium aus Milch oder Supplementen mit einem äquivalenten Gehalt des Mineralstoffs. Damit verbunden ist bei alkalischen Calciumwässern eine Hemmung der Knochenresorption. Auch senken bikarbonatreiche Wässer die renale Säurelast sowie die Calciumverluste über den Urin. Ungeklärt ist der Einfluss der Wässer auf die Calciumbilanz und das Frakturrisiko. Der Natrium- und Kaliumgehalt der meisten Wässer ist zu gering, um den Knochenstoffwechsel nennenswert beeinflussen zu können. Auch üben Wässer mit moderatem Fluoridgehalt (0,70-1,0 mg/l) keinen, von anderen Nahrungsfaktoren (Calcium, Protein) unabhängigen Einfluss auf die Mikrostruktur der Knochen aus.
Effects of a Regular Endurance Training Program on Running Economy and Biomechanics in Runners

Abstract A regular endurance training program may elicit different adaptations compared to an isolated training method. In this study, we analyzed the effects of 8 weeks of a regular endurance training program on running economy (RE), particularly neuromuscular and biomechanical parameters, in runners of different athletic abilities. Twenty-four male runners were divided into two groups: well-trained ( n= 12) and recreational ( n =12). Both groups completed a 4-min running bout at 13 and 17 km·h -1 , respectively, for the recreational and well-trained group, and a 5-jump plyometric test pre-post intervention. During the training program, participants completed low-intensity continuous sessions, high-intensity interval training sessions, and auxiliary strength training sessions. RE, measured as oxygen cost and energy cost, decreased by 6.15% (p=0.006) and 5.11% (p=0.043), respectively, in the well-trained group. In the recreational group, energy cost of running, respiratory exchange ratio, and leg stiffness decreased by 5.08% (p=0.035), 7.61% (p=0.003), and 10.59% (p=0.017), respectively, while ground contact time increased by 3.34% (p=0.012). The maximum height of the 5-jump plyometric test decreased by 4.55% (p=0.018) in the recreational group. We suggest that 8 weeks of regular endurance training leads to an improvement of ~5% in RE in recreational and well-trained runners with different physiological adaptations between groups and few changes in biomechanical and neuromuscular parameters only in recreational runners.
Direct patterning of functional materials using nanoimprint lithography

Nanoimprint lithography is a large area, high resolution and cost-effective replication technology for micro- and nanostructures. An interesting possibility in the nanoimprint process is the use of materials that remain a functional part of the final component or device. Such an additive approach offers interesting opportunities in terms of novel applications but also cost reduction and could also contribute to sustainability aspects. This paper is aiming at providing a short noncomprehensive overview on the direct patterning of various functional materials by using NIL for optics and life science applications.
Tragedy of the Commons in Crowd Work-Based Research

Academic scholars have leveraged crowd work platforms such as MTurk to conduct research and collect data, but the data quality crisis in crowd work has been an alarming phenomenon recently. Though prior studies have discussed data quality and validity issues in crowd work via surveys and experiments, they kind of neglected to explore the scholars’ and particularly the IRB's ethical concerns and the related policies in various ethical guidelines for crowd work-based research in these respects. In this study, we interviewed 17 scholars from six disciplines and 15 IRB directors and analysts in the U.S. and analyzed 28 research guidance documents to fill these gaps. We identified common themes among our interviewees and documents but also discovered distinctive and even opposing views regarding the approval rate, rejection, and internal/external research validity. Based on the findings, we discussed a potential Tragedy of the Commons regarding data quality deterioration and the disciplinary differences regarding validity in crowd work-based research. We further explored the origin of the data quality and validity issues in crowd work-based research. We advocated the IRB's ethical concerns in crowd work-based research be heard and respected further and be reflected in the ethical guidance for crowd work-based research. Finally, we proposed our research implications, limits, and future work.
When Games Become Inaccessible: A Constructive Grounded Theory on Stuckness in Videogames

A player feeling stuck is a player who risks abandoning a game and all their progress. Currently, this experience is an under-explored area in literature and is mostly approached from an expert perspective. A better understanding from a player’s perspective could bring new light on how to correctly identify when it happens and support the player in overcoming the obstacles. We particularly miss information if and how stuckness arises in different genres of games, as in the case of narrative or decision-making games where most goals will depend on the personal preference of the player. We present here a first qualitative study using a constructive grounded theory approach to understand how players experience stuckness. So far we conducted 9 interviews with players and contributed with 1) Thematic analysis of when and why stuckness arises with 37 examples. 2) An in-progress theory that demonstrated that stuckness is experienced in four phases (expectations, unprogress, evaluation, and resolution) and depends on the expectation of a fair and meaningful game. 3) Presenting different types of stuckness, including stuckness caused by expectation, game design balance, social interaction, or accessibility to the game challenge.
Yield Optimization for Analog Circuits over Multiple Corners via Bayesian Neural Networks: Enhancing Circuit Reliability under Environmental Variation

The reliability of circuits is significantly affected by process variations in manufacturing and environmental variation during operation. Current yield optimization algorithms take process variations into consideration to improve circuit reliability. However, the influence of environmental variations (e.g., voltage and temperature variations) is often ignored in current methods because of the high computational cost. In this article, a novel and efficient approach named BNN-BYO is proposed to optimize the yield of analog circuits in multiple environmental corners. First, we use a Bayesian Neural Network (BNN) to simultaneously model the yields and performances of interest in multiple corners efficiently. Next, the multi-corner yield optimization can be performed by embedding BNN into a Bayesian optimization framework. Since the correlation among yields and performances of interest in different corners is implicitly encoded in the BNN model, it provides great modeling capabilities for yields and their uncertainties to improve the efficiency of yield optimization. Our experimental results demonstrate that the proposed method can save up to 45.3% of simulation cost compared to other baseline methods to achieve the same target yield. In addition, for the same simulation cost, our proposed method can find better design points with 3.2% yield improvement.
Meaningful Play and Malicious Delight: Exploring Maldaimonic Game UX

Maldaimonia is a new experiential concept that refers to self-actualization and self-expression through egocentric, destructive, and/or exploitative activities. Still, it is unclear whether maldaimonia is an actual facet of real experience. As a subversive orientation, it may be rare or socially challenging to discuss openly. However, video games provide a space in which people can be expressive in different ways without the same repercussions as in real life. Indeed, game spaces may be one of the few contexts in which to study maldaimonic experiences. In this study, we examined whether and how maldaimonia exists as a feature of game user experiences by analyzing critical self-reports of gaming activities, confirming its existence. We contribute this new construct to work on "dark play" in games research.
Using VNIR and SWIR field imaging spectroscopy for drought stress monitoring of beech seedlings

Drought stress is expected to become a recurrent problem for central European forests due to regional climate change. In order to study the effects on one of the most common tree species in Germany, the European beech (Fagus sylvatica), young potted beech trees were exposed to drought stress in a controlled experiment and their reaction was observed using visible/near-infrared (VNIR) and shortwave infrared (SWIR) field imaging spectroscopy cameras mounted on a platform. Equivalent water thickness (EWT) and leaf chlorophyll content (LCC) were measured and partial least squares (PLS) regression models were trained using these reference measurements and reflectance spectra of the trees. The models were applied to create maps of these properties with a spatial resolution in the millimetre range. These maps can be used to study the spatial distribution of EWT and LCC for single leaves or even for intra-leaf variability. Both properties can be estimated using only the VNIR sensor, but EWT estimation improves considerably by also incorporating SWIR data. LCC estimations with SWIR data alone do not work satisfactorily.
Brain mechanism of foraging: reward-dependent synaptic plasticity or neural integration of values?

In foraging, behavior is guided by action values that are stored in memory and updated depending on the history of choices and rewards. What is the neural mechanism for action value maintenance and reward-dependent update? Here we explore two contrasting network models: neural integration and synaptic learning of action value. We show that both mechanisms reproduce existing experimental data, but they depend on distinct and falsiﬁable assumptions about the biological neural circuits. We demonstrate neural dynamical signatures and perturbations that could be carried out experimentally to differentiate the two contrasting scenarios.
The prion-like domain of the chloroplast RNA binding protein CP29A is required for cold-induced phase separation next to nucleoids and supports RNA splicing and translation during cold acclimation

Arabidopsis thaliana is capable of producing photosynthetic tissue with active chloroplasts at temperatures as low as 4°C, and this process depends on the presence of the nuclear-encoded, chloroplast-localized RNA-binding protein CP29A. In this study, we demonstrate that CP29A undergoes phase separation in vitro and in vivo in a temperature-dependent manner, which is mediated by a prion-like domain (PLD) located between the two RNA recognition motif (RRM) domains of CP29A. The resulting droplets display liquid-like properties and are found in close proximity to chloroplast nucleoids. The PLD is required to support chloroplast RNA splicing and translation in cold-treated tissue. Together, our findings suggest that plant chloroplast gene expression is compartmentalized by inducible condensation of CP29A at low temperatures, a mechanism that could play a crucial role for plant cold resistance.
Improved Resolution of Highly Pathogenic Avian Influenza Virus Haemagglutinin Cleavage Site Using Oxford Nanopore R10 Sequencing Chemistry

Highly pathogenic avian influenza viruses continue to pose global risks to One Health, including agriculture, public, and animal health. Rapid and accurate genomic surveillance is critical for monitoring viral mutations, tracing transmission, and guiding interventions in near real-time. Oxford Nanopore sequencing holds promise for real-time influenza genotyping, but data quality from R9 chemistry has limited its adoption due to challenges resolving low-complexity regions such as the biologically critical hemagglutinin cleavage site, a homopolymer of basic amino acids that distinguish highly pathogenic strains. In this study, human and avian influenza isolates (n=45) from Cambodia were sequenced using both R9.4. 1 and R10.4. 1 flow cells and chemistries to evaluate performance between approaches. Overall, R10.4. 1 yielded increased data output with higher average quality compared to R9.4. 1, producing improved consensus sequences using a reference-based bioinformatics approach. R10.4. 1 had significantly lower minor population insertion and deletion frequencies, driven by improved performance in low sequence complexity regions prone to insertion and deletion errors, such as homopolymers. Within the hemagglutinin cleavage site, R10.4. 1 resolved the correct motif in 90% of genomes compared to only 60% with R9.4. 1. Further examination showed reduced frameshift mutations in consensus sequences generated with R10.4. 1 that could result in incorrectly classified virulence. Improved consensus genome quality from nanopore sequencing approaches, especially across biologically important low-complexity regions, is critical to reduce subjective hand-curation and will improve local and global genomic surveillance responses.
The Pronunciation of English in South Africa

There is no one, typical South African English accent as there is one overall Australian English accent. The variety of accents within the society is in part a consequence of the varied regional origins of groups of native English speakers who came to Africa at different times, and in part a consequence of the variety of mother tongues of the different ethnic groups who today use English so extensively that they must be included in the English-using community.