Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring impact of recombination landscapes on breeding outcomes

Significance Crossing-over is a process of mixing chromosomes from mother and father to create new combinations of traits in the progeny. Plant breeders rely on it to produce new crop varieties with improved yields, resistances to new pests, and tolerance to extreme environmental conditions. Unfortunately, crossing-over events in crops are rare and do not always occur in places where breeders need them most. Thus, several methods have been developed to increase the number of crossing-over events and ensure that they occur at desired genome locations. We review these technologies and use simulations to show that they indeed can be helpful in plant breeding programs. We also discuss what needs to be done to implement these methods in breeding practice.
Analytical Study of the Evolution of an Amplifying Baroclinic Wave.

Abstract An analytical study is made showing how second-order, non-geostrophic effects can modify a two-layer baroclinic wave system that grows exponentially from a small perturbation in a uniform zonal current. Many of the features observed on weather maps are seen to develop, including the relative meridional displacements and intensifications of the high and low pressure areas, the formation of a cutoff low aloft with a splitting of the jet stream, and the formation of zones of strong temperature gradient representing mid-tropospheric “fronts. ” An analysis is also given to show the role of shear of the basic zonal current in the development of horizontal tilts of the amplifying waves.
PFAS Contamination: Pathway from Communication to Behavioral Outcomes

ABSTRACT Guided by the risk information seeking and processing model, this study examines social cognitive variables that motivate individuals to actively seek and process information related to per- and polyfluoroalkyl substances (PFAS) contamination. Results indicate that information insufficiency, affective response, and informational subjective norms are positively related to information seeking and systematic processing, which are positively associated with policy support and intention to adopt risk mitigation behaviors. These findings suggest that when communicating the health risks of PFAS contamination to the general public, cognitive, affective, and normative factors are important initial steps to generate public interest in relevant information.
Acute on chronic liver failure: prognostic models and artificial intelligence applications

Critically ill patients presenting with acute on chronic liver failure (ACLF) represent a particularly vulnerable population due to various considerations surrounding the syndrome definition, lack of robust prospective evaluation of outcomes, and allocation of resources such as organs for transplantation. Ninety-day mortality related to ACLF is high and patients who do leave the hospital are frequently readmitted. Artificial intelligence (AI), which encompasses various classical and modern machine learning techniques, natural language processing, and other methods of predictive, prognostic, probabilistic, and simulation modeling, has emerged as an effective tool in various areas of healthcare. These methods are now being leveraged to potentially minimize physician and provider cognitive load and impact both short-term and long-term patient outcomes. However, the enthusiasm is tempered by ethical considerations and a current lack of proven benefits. In addition to prognostic applications, AI models can likely help improve the understanding of various mechanisms of morbidity and mortality in ACLF. Their overall impact on patient-centered outcomes and countless other aspects of patient care remains unclear. In this review, we discuss various AI approaches being utilized in healthcare and discuss the recent and expected future impact of AI on patients with ACLF through prognostic modeling and AI-based approaches.
A new Whitney-based material operator for the finite-integration technique on triangular grids

We propose a new matrix operator for the material relations within the finite-integration technique. It is based on the assumption of Whitney-type basis functions in the cells of a triangular two-dimensional grid. To ensure the symmetry of the new operator, we introduce the positions of the dual points in each primary cell as additional degrees of freedom in the derivation of the discretization scheme. It is shown that there exists one unique position, which leads to symmetric material matrices - a sufficient condition for the stability of the method. In addition, the analysis may help to understand the differences between finite-integration and finite-element schemes on triangular grids.
Short- and long-term risks of photoselective laser vaporization of the prostate: a population-based comparison with transurethral resection of the prostate

Abstract Background Transurethral resection of the prostate (TURP) is the standard surgical treatment for benign prostate enlargement (BPE). Photoselective vaporization of the prostate (PVP) is an alternative, but there is limited real-life evidence of PVP risks. Objective To compare short- and long-term risks of PVP to those of TURP in the treatment of BPE. Materials and methods Consecutive patients who underwent elective PVP or TURP between 2006 and 2018 in 20 hospitals in Finland were retrospectively studied using a combination of national registries (n = 27,408; mean age 71 years). Short-term risks were postoperative mortality, major adverse cardiovascular events (MACE), and reoperations for bleeding. Long-term risks were reoperations for BPE or any urethral operations within 12 years. Differences between treatment groups were balanced by inverse probability of treatment weighting. Risks were analyzed using the Kaplan–Meier method and Cox regression. Results There were no differences in postoperative mortality or MACE between the study groups. Reoperations for bleeding were less frequent after PVP (0.9%, HR: 0.72, p = 0.042). Bleeding was more likely in patients with atrial fibrillation (number needed to treat [NNT] for PVP vs TURP: 61). Cumulative incidence for reoperation was higher after PVP (23.5%) than after TURP in long-term follow-up (17.8%; HR: 1.20, p < 0.0001, NNT: −31.7). Conclusions PVP is associated with lower postoperative bleeding risk but higher long-term reoperation risk than TURP. Patients with high bleeding risk and a low likelihood of needing reoperation appear most suitable for laser vaporization. KEY MESSAGE PVP is associated with lower postoperative bleeding risk but higher long-term reoperation risk than TURP. PVP appears an attractive treatment option, especially for patients with high bleeding risk and a low likelihood of needing a reoperation.
The Garden City, Kansas, Storm during VORTEX 95. Part II: The Wall Cloud and Tornado

Abstract On 16 May 1995, a supercell storm produced an F1 tornado near Garden City, Kansas, during VORTEX (Verification of the Origins of Rotation in Tornadoes Experiment). This event provided the first opportunity to synthesize data collected by a new airborne radar platform called ELDORA (Electra Doppler radar) developed by the National Center for Atmospheric Research. The evolution of the low- and midlevel mesocyclone was presented in a companion paper. In this paper, the sequence of events that triggered tornadogenesis within the mesocyclone circulation is shown. The occlusion downdraft, documented in Part I, appears to promote “vortex breakdown” resulting in the generation of multiple vorticity centers. It is one of these centers that intensifies into the Garden City tornado. The structural relationship between the observed wall cloud and the radar reflectivity associated with the developing hook echo and the kinematic wind field is also presented. Although the wall cloud appears to be uniform there .
The Commensal Anaerobe Veillonella dispar Reprograms Its Lactate Metabolism and Short-Chain Fatty Acid Production during the Stationary Phase

Short-chain fatty acids produced by gut commensal bacteria play an important role in human physiology. Gut Veillonella and the metabolites acetate and propionate, produced by lactate fermentation, are associated with human health. ABSTRACT Veillonella spp. are obligate, anaerobic, Gram-negative bacteria found in the human oral cavity and gut. Recent studies have indicated that gut Veillonella promote human homeostasis by producing beneficial metabolites, specifically short-chain fatty acids (SCFAs), by lactate fermentation. The gut lumen is a dynamic environment with fluctuating nutrient levels, so the microbes present shifting growth rates and significant variations of gene expression. The current knowledge of lactate metabolism by Veillonella has focused on log phase growth. However, the gut microbes are mainly in the stationary phase. In this study, we investigated the transcriptomes and major metabolites of Veillonella dispar ATCC 17748T during growth from log to stationary phases with lactate as the main carbon source. Our results revealed that V. dispar reprogrammed its lactate metabolism during the stationary phase. Lactate catabolic activity and propionate production were significantly decreased during the early stationary phase but were partially restored during the stationary phase. The propionate/acetate production ratio was lowered from 1.5 during the log phase to 0.9 during the stationary phase. Pyruvate secretion was also greatly decreased during the stationary phase. Furthermore, we have demonstrated that the gene expression of V. dispar is reprogrammed during growth, as evidenced by the distinct transcriptomes present during the log, early stationary, and stationary phases. In particular, propionate metabolism (the propanediol pathway) was downregulated during the early stationary phase, which explains the decrease in propionate production during the stationary phase. The fluctuations in lactate fermentation during the stationary phase and the associated gene regulation expand our understanding of the metabolism of commensal anaerobes in changing environments. IMPORTANCE Short-chain fatty acids produced by gut commensal bacteria play an important role in human physiology. Gut Veillonella and the metabolites acetate and propionate, produced by lactate fermentation, are associated with human health. Most gut bacteria in humans are in the stationary phase. Lactate metabolism by Veillonella spp. during the stationary phase is poorly understood and was therefore the focus of the study. To this end, we used a commensal anaerobic bacterium and explored its short-chain fatty acid production and gene regulation in order to provide a better understanding of lactate metabolism dynamics during nutrient limitation.
Evidence for Phosphorylation-Dependent, Dynamic, Regulation of mGlu5 and Homer2 in Expression of Cocaine Aversion in Mice

Abstract Cocaine-induced changes in the expression of the glutamate-related scaffolding protein Homer2 influence this drug’s psychostimulant and rewarding properties. In response to neuronal activity, Homer2 is phosphorylated on S117/S216 by calcium-calmodulin kinase IIα (CaMKIIα), which induces a rapid dissociation of mGlu5-Homer2 scaffolds. Herein, we examined the requirement for Homer2 phosphorylation in cocaine-induced changes in mGlu5-Homer2 coupling, to include behavioral sensitivity to cocaine. For this, mice with alanine point mutations at (S117/216)-Homer2 (Homer2AA/AA) were generated, and we determined their affective, cognitive and sensorimotor phenotypes, as well as cocaine-induced changes in conditioned reward and motor hyperactivity. The Homer2AA/AA mutation prevented activity-dependent phosphorylation of S216 Homer2 in cortical neurons, but Homer2AA/AA mice did not differ from wild-type (WT) controls with respect to Morris maze performance, acoustic startle, spontaneous or cocaine-induced locomotion. Homer2AA/AA mice exhibited signs of hypoanxiety similar to the phenotype of transgenic mice with a deficit in signal-regulated mGluR5 phosphorylation (Grm5AA/AA). However, opposite of Grm5AA/AA mice, Homer2AA/AA mice were less sensitive to the aversive properties of high-dose cocaine under both place-conditioning and taste-conditioning procedures. Acute injection with cocaine caused dissociation of mGluR5 and Homer2 in striatal lysates from WT, but not Homer2AA/AA mice, suggesting a molecular basis for the deficit in cocaine aversion. These findings indicate that CaMKIIα-dependent phosphorylation of Homer2 gates the negative motivational valence of high-dose cocaine via regulation of mGlu5 binding, furthering an important role for dynamic changes in mGlu5-Homer interactions in addiction vulnerability.
Compliance Assessment of Tobacco Products to Cigarettes and Other Tobacco Products Act in India with Reference to Third Amendment Rules, 2020

Objective: Tobacco use is associated with mortality in low- and middle-income countries including India with dual burden of smoking and smokeless tobacco (SLT). Aligning with the FCTC, India has made substantial amendments in strengthening graphic warning under Cigarettes and Other Tobacco Products Act (COTPA) for sections 7,8 9 and “Specified warning”. Compliance assessment studies are necessary to understand current status of implementation for packaging laws. This study aimed to assess the compliance of COTPA sections 7,8 9 and Cigarettes and other Tobacco Products (Packaging and Labelling) Third Amendment Rules, 2020 in Delhi. Methods: Cross-sectional study was conducted in two districts of Delhi selected by simple random sampling. Fifteen points of sales were selected from each district through purposive sampling and 57 smoking and smokeless tobacco products were collected with Indian and foreign origin. An observation checklist for product analysis was prepared and pack analysis done based on COTPA sections 7,8 and 9 along with Third Amendment,2020 which included pictures and warnings to be circulated in 2021. Result: Total 57 samples has smoking (49.1%), smokeless (50.9%) with no SLT product of foreign origin. SLT and foreign products had low compliance of Section 7 and third amendment 2020 rules which includes manufacturing date and origin. Indian smoking products were highly compliant to section 8 and 9 whereas foreign and SLT products showed low compliance to section 8. COTPA Third Amendment Rules (2020) compliance was seen in Indian products with regards to SW (68.4%), PW (61.4%) and quit line (78.9%) with no compliance at all for foreign products. Conclusion: Foreign brands and SLT products had low compliance with sections 7 and 8 of COTPA and its amendments (2020). Compliance with illicit trade and SW needs regulation and strict implementation of law for SLT products.
Interspecies Interactions within the Host: the Social Network of Group B Streptococcus

Group B Streptococcus (GBS) is a pervasive neonatal pathogen accounting for a combined half a million deaths and stillbirths annually. The most common source of fetal or neonatal GBS exposure is the maternal microbiota. ABSTRACT Group B Streptococcus (GBS) is a pervasive neonatal pathogen accounting for a combined half a million deaths and stillbirths annually. The most common source of fetal or neonatal GBS exposure is the maternal microbiota. GBS asymptomatically colonizes the gastrointestinal and vaginal mucosa of 1 in 5 individuals globally, although its precise role in these niches is not well understood. To prevent vertical transmission, broad-spectrum antibiotics are administered to GBS-positive mothers during labor in many countries. Although antibiotics have significantly reduced GBS early-onset neonatal disease, there are several unintended consequences, including an altered neonatal microbiota and increased risk for other microbial infections. Additionally, the incidence of late-onset GBS neonatal disease remains unaffected and has sparked an emerging hypothesis that GBS-microbe interactions in developing neonatal gut microbiota may be directly involved in this disease process. This review summarizes our current understanding of GBS interactions with other resident microbes at the mucosal surface from multiple angles, including clinical association studies, agriculture and aquaculture observations, and experimental animal model systems. We also include a comprehensive review of in vitro findings of GBS interactions with other bacterial and fungal microbes, both commensal and pathogenic, along with newly established animal models of GBS vaginal colonization and in utero or neonatal infection. Finally, we provide a perspective on emerging areas of research and current strategies to design microbe-targeting prebiotic or probiotic therapeutic intervention strategies to prevent GBS disease in vulnerable populations.
Stability tests for one- two- and multidimensional linear systems

The paper reviews analytical stability tests for 1-dimensional linear systems since the early tests of E.J. Routh in his famous Adams Prize essay of 1877. The historical background of Routh's stability test and criterion, as well as Fuller's conjecture on its simplification, will be mentioned. In the historical review, the works of Hermite, Sylvester, Maxwell and others as related to the stability problem are also discussed. This review provides the context for a discussion of recent stability tests obtained for 2-dimensional and multidimensional linear systems. These tests are described and their computational complexity discussed in detail. In addition, the applications of stability testing to the study of 2- and multidimensional digital filters, numerical analysis of stiff-differential equations, realisation of mixed lumped- and distributed parameter systems, and the design of output feedback systems will be briefly mentioned. Comments on future research in this area conclude the review.
Stability and stabilization of time-delay systems

Moreover, I am grateful to Brigitte Rohrbach for her careful editing of the manuscript which helped improve the standard of my English. Finally, a special thank to my wife Franziska for her patience and invaluable support. vii Summary The stability analysis of time-delay systems forms the centre of this work. Three tools are typically used to investigate the stability of such systems: Razumikhin theory, Lyapunov-Krasovskii theory, and (for linear time-delay systems) eigenvalue considerations. However, none of these basic concepts represents applicable stability tests in terms of the system matrices. Therefore , based on the three stability concepts mentioned some suitable algebraic stability tests are developed in this work. The stability tests obtained can be categorized into four groups, depending on how much information concerning the delays is required for these tests: • Delay-independent stability criteria: The length of the delay need not be known for the application of these stability tests. The delays may be state-dependent and/or time variable. The only assumption needed is that the delays are continuous and bounded. • Stability criteria independent of constant delays: In the second group it is assumed that the delays of the system are constant; no further information on the delays is necessary. • Stability criteria independent of a delay constant: This type of stability criteria presumes that the delays are constant and that the ratios of size of the delays are known. • Delay-dependent stability criteria: This group includes exact algebraic stability criteria depending on the delay and on the system constants and stability criteria which yield an upper bound of the admissible delay. The need for delay-independent (and related) stability tests is obvious, since in practice the delays are difficult to estimate, especially those that are time variable and state dependent. While algebraic stability tests independent of delays are suitable to apply, exact algebraic stability conditions depending on the delay and the system constants are known only in some special cases. In this context a method is presented to achieve some extensions. The method permits the investigation of the stability of systems which are general enough to demonstrate the differences among the four types of stability tests. The stability of general, linear time-delay systems, however, can be checked exactly only by eigenvalue considerations. Unfortunately, the computation of viii the eigenvalues is a cumbersome task, since the corresponding transcen-dental characteristic equation contains exponential terms which induce extreme gradients. An improved version …
RHO OF PLANT proteins are essential for pollen germination in Arabidopsis.

Pollen germination is a process of polarity establishment, through which a single and unique growth axis is established. Although most of the intracellular activities associated with pollen germination are controlled by RHO OF PLANTs (ROPs) and increased ROP activation accompanies pollen germination, a critical role of ROPs in this process has not yet been demonstrated. Here, by genomic editing of all four Arabidopsis (Arabidopsis thaliana) ROPs that are preferentially expressed in pollen, we showed that ROPs are essential for polarity establishment during pollen germination. We further identified and characterized two ROP effectors in pollen germination (REGs) through genome-wide interactor screening, Boundary of ROP domain (BDR) members BDR8 and BDR9, whose functional loss also resulted in no pollen germination. BDR8 and BDR9 were distributed in the cytosol and the vegetative nucleus of mature pollen grains but re-distributed to the plasma membrane (PM) of the germination site and to the apical PM of growing pollen tubes. We demonstrated that the PM re-distribution of BDR8 and BDR9 during pollen germination relies on ROPs but not vice versa. Furthermore, enhanced expression of BDR8 partially restored germination of rop1 pollen but had no effects on that of the quadruple rop pollen, supporting their genetic epistasis. Results presented here demonstrate an ROP signaling route essential for pollen germination, which supports evolutionarily conserved roles of Rho GTPases in polarity establishment.
Atrial Appendage Aneurysms: Natural History and Outcomes

Background Left (LAAA) and right atrial appendage aneurysms (RAAA) are rare entities, and their natural history, management, and long-term outcomes are not well studied. Methods This retrospective review includes all patients from 2000 to 2021 with atrial appendage aneurysms at our institution identified using an electronic search tool. LAAA and RAAA were confirmed using multimodality imaging and intraoperative findings. Results We identified 13 (87%) patients with LAAA and 2 (13%) with RAAA. At diagnosis, 11 (73%) were female, mean age was 51.4 ± 18.8 years, and ejection fraction 56.5 ± 13.1%. Three (20%) patients had congenital heart disease including 2 (13%) with atrioventricular septal defects and 1 (7%) with congenitally corrected transposition. LAAA/RAAA was diagnosed due to new-onset atrial fibrillation (AF) in 6 (40%) patients and embolic stroke in 2 (13%). Ten patients had preexisting AF diagnosed 2.9 ± 1.4 years earlier at a mean age of 50.2 ± 15.5 years. Thrombus within the aneurysm was identified in 2 (15%) LAAA patients. All patients were on anticoagulation and follow-up of the cohort from diagnosis was 7.1 ± 6.2 years. Eleven (73%) patients were surgically managed with 7 (64%) lesions excised, 1 (9%) stapled, and 3 (27%) ligated. Postoperative complications occurred in 2 (18%) patients with 1 (7%) developing tricuspid regurgitation and another with pericardial effusion and tamponade. Conclusions Atrial appendage aneurysm is a rare disease and nearly half of patients present with AF. Surgical treatment with concomitant AF ablation is a reasonable and safe management option.