Miracle-dz/UniFAR-FTUs huggingface dataset:
Chile Pepper (Capsicum) Breeding and Improvement in the “Multi-Omics” Era

Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have “defined” the state of New Mexico, USA. The official state question, “Red or Green? ” refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in “multi-omics,” that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.
Downregulation of LHCGR Attenuates COX-2 Expression and Induces Luteinized Unruptured Follicle Syndrome in Endometriosis

An association between endometriosis and luteinized unruptured follicle syndrome (LUFs) has long been identified. Although inactivating mutation of luteinizing hormone/choriogonadotropin receptor (LHGCR) results in LUFs, whether LHCGR contributes to promoting LUFs in endometriosis remains elusive. To investigate the effect of LHCGR signaling in the development of endometriosis-associated LUFs and dissect the underlying mechanism in vivo mouse endometriosis model was established to measure the effect on ovarian folliculogenesis. In vitro cultures of primary human GCs collected from patients undergoing in vitro fertilization were performed and treated with human chorionic gonadotropin (hCG), dibutyryl cyclic-AMP (db-cAMP), LHCGR or CCAAT/enhancer binding protein-α (C/EBPα) small interfering RNA to identify the potential mechanisms. KGN cell line was used to investigate the mechanistic features of transcriptional regulation. Results showed an increased incidence of LUFs was observed in mice with endometriosis. The expression of LHCGR was decreased in the GCs of endometriosis mice. In in vitro cell models, LHCGR signaling increased the expression of C/EBPα and cyclooxygenase-2(COX-2), while inhibiting C/EBPα mitigated the induced COX-2 expression. Mechanically, C/EBPα bounded to the promoter region of COX-2 and increased the transcriptional activity under the stimulation of hCG or db-cAMP. Taken together, this study demonstrated that the LHCGR signaling was reduced in GCs of endometriosis and resulted in a decrease in gonadotropin-induced COX-2 expression. Our study might provide new insights into the dysfunction of GCs in endometriosis.
Associations of Parity With Change in Global Cognition and Incident Cognitive Impairment in Older Women

Background The evidence of the association between parity and risk of mild cognitive impairment (MCI) or dementia is mixed, and the relationship between parity and longitudinal cognitive changes is less clear. We investigated these issues in a large population of older women who were carefully monitored for development of MCI and probable dementia. Methods Using the Women’s Health Initiative Memory Study, 7,100 postmenopausal women (mean age 70.1 ± 3.8 years) with information on baseline parity (defined as the number of term pregnancies), measures of global cognition (Modified Mini-Mental State Examination score) from 1996–2007, and cognitive impairment (centrally adjudicated diagnoses of MCI and dementia) from 1996–2016 were included. Multivariable linear mixed-effects models were used to analyze the rate of changes in global cognition. Cox regression models were used to evaluate the risk of MCI/dementia across parity groups. Results Over an average of 10.5 years, 465 new cases of MCI/dementia were identified. Compared with nulliparous women, those with a parity of 1–3 and ≥4 had a lower MCI/dementia risk. The HRs were 0.75 (0.56–0.99) and 0.71 (0.53–0.96), respectively (P < 0.01). Similarly, a parity of 1–3 and ≥4 was related to slower cognitive decline (β = 0.164, 0.292, respectively, P < 0.05). Conclusion Higher parity attenuated the future risk for MCI/dementia and slowed the rates of cognitive decline in elderly women. Future studies are needed to determine how parity affects late-life cognitive function in women.
Current Progress in Optimising Sustainable Energy Recovery From Cattle Paunch Contents, a Slaughterhouse Waste Product

Paunch contents are the recalcitrant, lignocellulose-rich, partially-digested feed present in the rumen of ruminant animals. Cattle forage in Europe is primarily from perennial and Italian ryegrasses and/or white clover, so paunch contents from forage-fed cattle in Europe is enriched in these feedstuffs. Globally, due to its underutilisation, the potential energy in cattle paunch contents annually represents an energy loss of 23,216,548,750–27,804,250,000 Megajoules (MJ) and financial loss of up to ~€800,000,000. Therefore, this review aims to describe progress made to-date in optimising sustainable energy recovery from paunch contents. Furthermore, analyses to determine the economic feasibility/potential of recovering sustainable energy from paunch contents was carried out. The primary method used to recover sustainable energy from paunch contents to-date has involved biomethane production through anaerobic digestion (AD). The major bottleneck in its utilisation through AD is its recalcitrance, resulting in build-up of fibrous material. Pre-treatments partially degrade the lignocellulose in lignocellulose-rich wastes, reducing their recalcitrance. Enzyme systems could be inexpensive and more environmentally compatible than conventional solvent pre-treatments. A potential source of enzyme systems is the rumen microbiome, whose efficiency in lignocellulose degradation is attracting significant research interest. Therefore, the application of rumen fluid (liquid derived from dewatering of paunch contents) to improve biomethane production from AD of lignocellulosic wastes is included in this review. Analysis of a study where rumen fluid was used to pre-treat paper sludge from a paper mill prior to AD for biomethane production suggested economic feasibility for CHP combustion, with potential savings of ~€11,000 annually. Meta-genomic studies of bacterial/archaeal populations have been carried out to understand their ruminal functions. However, despite their importance in degrading lignocellulose in nature, rumen fungi remain comparatively under-investigated. Further investigation of rumen microbes, their cultivation and their enzyme systems, and the role of rumen fluid in degrading lignocellulosic wastes, could provide efficient pre-treatments and co-digestion strategies to maximise biomethane yield from a range of lignocellulosic wastes. This review describes current progress in optimising sustainable energy recovery from paunch contents, and the potential of rumen fluid as a pre-treatment and co-substrate to recover sustainable energy from lignocellulosic wastes using AD.
Cultural Sensitivity in Preventive Infant Mental Health Care: An Example From the Developmental Guidance Project FIRST STEPS in Belgium

Preventive developmental guidance programmes have been applied on a large scale for several decades now in many western countries. But how do we adapt these programs to families with very different ethnic backgrounds? How can we concretise the concept of cultural sensitivity into that context? The plea of von Klitzing, the former President of the World Association for Infant Mental Health, for von Klitzing for further reflection on the concretization of cultural sensitivity in the context of infant mental health care is the main source of inspiration to this article. von Klitzing speaks out against the point of view in which universal children’s rights or conditions that are seen as promoting a child’s development all around the globe, are criticized as being only western conceptions and thereby culturally biassed. Following this kind of reasoning, a culturally relativistic stance on what a facilitating environment is, should be adopted. Such a discussion in terms of universalism versus relativism, though, as argues von Klitzing, is an old antagonism that cannot inspire us for the adaptation of early health care practices or developmental guidance programs that are fitting in to the needs of families and their babies that are living in multicultural contexts. Although it could be interesting to think about how certain universal principles of good-enough child care can be formulated or embodied in an intercultural variety of ways, these variable expressions of the worldwide agreed upon principles of good early mental health care will only be culture-specific translations of these universal principles. They can’t in any way be seen as an argument against the universality of these principles, as argues von Klitzing, who is describing another way of solving the problem of the cultural relativist criticism on the universality of principles of good infant mental health: culture sensitive infant mental health services. But, to make the principle of cultural sensitivity work in practice, we need to fill it with content. This article is mainly on what it concretely means to work in a culture sensitive way in our preventive practice within the FIRST STEPS program, a Belgian project for immigrant and exiled mothers and their children from zero to three.
NtNAC053, A Novel NAC Transcription Factor, Confers Drought and Salt Tolerances in Tobacco

The NAC (NAM, ATAF1/2, and CUC2) family acts as one of the largest families of the transcription factor in the plant kingdom and was revealed to function as the important regulators in various environmental stresses. However, a few studies were reported about the biofunctions of the NAC transcription factor in tobacco. In the current study, we characterized a novel NAC transcription factor encoding the gene NtNAC053 in tobacco, which was significantly up-regulated when exposed to salt and drought treatments. The results of cis-acting elements analysis suggested that the promoter region of NtNAC053 gene possesses a number of stress-responsive elements, and this gene could be induced by exogenous abscisic acid (ABA) treatment. Moreover, the NtNAC053–GFP fusion protein was localized in the cell nucleus and possessed a transactivation domain in its C-terminal, implying that NtNAC053 may undertake as a transcriptional activator in tobacco. Notably, the overexpression of NtNAC053 in tobacco resulted in hypersensitivity to ABA treatment. Furthermore, these overexpression lines showed significantly enhanced tolerances to drought and salt stresses. Under salt and drought stresses, these overexpression lines possessed higher superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities. Interestingly, the expressions of putative stress-related genes, including NtCOR15A, NtRAB18, NtDREB1A, NtERF5, NtKAT2, and NtERD11, were up-regulated in these overexpression lines when subjected to salt and drought stresses. The clues provided in our study suggested that the NtNAC053 gene encodes a novel NAC transcription factor and could confer the drought and salt stress tolerances by inspiring the downstream stress-responsive genes and antioxidant system in tobacco.
Clinical Impact of Hydroxyapatite on the Outcome of Skull Base Reconstruction for Intraoperative High-Flow CSF Leak: A Propensity Score Matching Analysis

Background Despite recent advances in skull base reconstructive techniques, including the multilayer technique during the last decade, complete reconstruction of grade 3 intraoperative high-flow cerebrospinal fluid (CSF) leak remains challenging. This study was designed to investigate the role of injectable hydroxyapatite (HXA) used in the multilayer technique on the clinical outcome of skull base reconstruction for intraoperative high-flow CSF leak. Materials and Methods This study enrolled 187 patients who experienced intraoperative high-flow CSF leak after endoscopic endonasal surgery for anterior skull base or suprasellar pathologies between January 2014 and July 2021. All skull base defects were reconstructed using the conventional multilayer technique including a vascularized naso-septal flap (NSF, n = 141) and the combined use of HXA with the conventional multilayer technique (HXA group, n = 46). We retrospectively evaluated the efficacy of the HXA group by 1:2 propensity score matching analysis. Results Overall, 17 of 187 patients (9.1%) showed postoperative CSF leaks, resulting in second reconstruction surgery. There were no statistical differences in patient age, sex, body mass index, tumor location, tumor type, and degree of resection, except for the follow-up period between the two groups. The HXA group showed a significantly lower incidence of postoperative CSF leak than the control group (0% vs. 12.1%, p < 0.05). Postoperative lumbar drain (LD) was performed in 8.7% of the HXA group compared to 46.1% of the control group (p < 0.01). CSF leak-related infection rates showed a decreasing tendency in the HXA group compared to the control group (0 vs. 7.1%, p = 0.06). A total of 46 patients in the HXA group were well matched with the control group (92 patients) at a 1:2 ratio. In the propensity score-matched control group, there were higher rates of postoperative CSF leaks than in the HXA group. Conclusion The use of HXA combined with the conventional multilayer technique completely reduced postoperative CSF leaks in this study. This technique resulted in reduced CSF leakage, even without postoperative LD, and decreased infection rates. Further randomized comparative studies are required to confirm our findings.
Earthquake Productivity Law in a Wide Magnitude Range

Earthquakes are usually followed by aftershocks. The number of aftershocks—the so-called productivity—depends on the magnitude of the earthquake. In seismic modeling it is usually assumed that the number of aftershocks is approximately the same for earthquakes with the same magnitude. This is one of the key assumptions on which the calculations are based. Although it is known that in reality this number can vary widely, only recently a pattern of such changes, called the earthquake productivity law, has been established. If we consider only direct aftershocks in a fixed magnitude range relative to the magnitude of the main shocks, then their number for a set of earthquakes in some spatiotemporal volume has an exponential distribution form. This means that fewer aftershocks are more likely. The most likely outcome is the complete absence of aftershocks. This pattern is quite counterintuitive, especially when considering aftershocks over a wide range of magnitudes. Here we managed to confirm the fulfillment of the earthquake productivity law for the wide range of magnitudes. For earthquakes of magnitude 6 and higher in the land part of Japan, it is confirmed that the frequency distribution of the number of their direct aftershocks with a minimum magnitude of 5 units less has an exponential shape. In seismicity modeling the validated earthquake productivity law makes it possible to replace the incorrect assumption of constant earthquake productivity with an exponential distribution. The single parameter of this regularity is easily determined from the actual data.
Winter Bird Diversity and Abundance in Small Farmlands in a Megacity of Southern China

Urban expansion often accompanies a loss of natural habitats and arable lands but an increase in urban population. In China, vegetable-dominant small farmlands are common in urban/peri-urban areas. Some farmlands are also associated with government policy that aims to enhance local farmers’ livelihoods as well as increase food availability for city citizens. While small urban farmlands create open greenery cover that may provide birds with resources such as food and shelter, little attention has been given to understanding bird diversity in urban farmlands. Using two hierarchical models (multi-species occupancy model and N-mixture model), we examined how species richness and abundance of birds were associated with environmental characteristics within and surrounding urban farmlands in Guangzhou, one of the largest cities in China. We conducted crop and bird surveys at urban farmlands during two winter seasons between December 2019 and January 2021. Species richness increased with non-woody (herbaceous) vegetation cover within a farmland. Abundance of three species was also positively associated with the local non-woody vegetation variable. Two species were more abundant at farmlands with higher crop diversity. Compositional features of matrix surrounding a farmland (a 500-m circular area) did not affect species richness. However, species richness and abundance of one species tended to decrease with increasing farmland fragmentation (patch density of farmlands) within a 1-km circular area. These findings suggest that (1) birds could be more influenced by environmental features within farmlands than matrix features surrounding farmlands, (2) local uncultivated herbaceous vegetation is an important environmental feature, and (3) diverse crops in farmlands may benefit some birds. They also indicate that the landscape pattern of farmlands, such as degree of fragmentation, could affect bird diversity in urban farmlands.
First Demonstration of Functional Task Performance Using a Sonomyographic Prosthesis: A Case Study

Ultrasound-based sensing of muscle deformation, known as sonomyography, has shown promise for accurately classifying the intended hand grasps of individuals with upper limb loss in offline settings. Building upon this previous work, we present the first demonstration of real-time prosthetic hand control using sonomyography to perform functional tasks. An individual with congenital bilateral limb absence was fitted with sockets containing a low-profile ultrasound transducer placed over forearm muscle tissue in the residual limbs. A classifier was trained using linear discriminant analysis to recognize ultrasound images of muscle contractions for three discrete hand configurations (rest, tripod grasp, index finger point) under a variety of arm positions designed to cover the reachable workspace. A prosthetic hand mounted to the socket was then controlled using this classifier. Using this real-time sonomyographic control, the participant was able to complete three functional tasks that required selecting different hand grasps in order to grasp and move one-inch wooden blocks over a broad range of arm positions. Additionally, these tests were successfully repeated without retraining the classifier across 3 hours of prosthesis use and following simulated donning and doffing of the socket. This study supports the feasibility of using sonomyography to control upper limb prostheses in real-world applications.
The Interaction Between Nitrogen Supply and Light Quality Modulates Plant Growth and Resource Allocation

Nitrogen availability and light quality affect plant resource allocation, but their interaction is poorly understood. Herein, we analyzed the growth and allocation of dry matter and nitrogen using lettuce (Lactuca sativa L.) as a plant model in a factorial experiment combining three light regimes (100% red light, R; 50% red light + 50% blue light, RB; 100% blue light, B) and two nitrogen rates (low, 0.1 mM N; high, 10 mM N). Red light increased shoot dry weight in relation to both B and RB irrespective of nitrogen supply. Blue light favored root growth under low nitrogen. Allometric analysis showed lower allocation to leaf in response to blue light under low nitrogen and similar leaf allocation under high nitrogen. A difference in allometric slopes between low nitrogen and high nitrogen in treatments with blue light reflected a strong interaction effect on root-to-shoot biomass allocation. Shoot nitrate concentration increased with light exposure up to 14 h in both nitrogen treatments, was higher under blue light with high nitrogen, and varied little with light quality under low nitrogen. Shoot nitrogen concentration, nitrogen nutrition index, and shoot NR activity increased in response to blue light. We conclude that the interaction between blue light and nitrogen supply modulates dry mass and nitrogen allocation between the shoot and root.
Tracking the Effect of Therapy With Single-Trial Based Classification After Stroke

Stroke is a debilitating disease that leads, in the 50% of cases, to permanent motor or cognitive impairments. The effectiveness of therapies that promote recovery after stroke depends on indicators of the disease state that can measure the degree of recovery or predict treatment response or both. Here, we propose to use single-trial classification of task dependent neural activity to assess the disease state and track recovery after stroke. We tested this idea on calcium imaging data of the dorsal cortex of healthy, spontaneously recovered and rehabilitated mice while performing a forelimb retraction task. Results show that, at a single-trial level for the three experimental groups, neural activation during the reward pull can be detected with high accuracy with respect to the background activity in all cortical areas of the field of view and this activation is quite stable across trials and subjects of the same group. Moreover, single-trial responses during the reward pull can be used to discriminate between healthy and stroke subjects with areas closer to the injury site displaying higher discrimination capability than areas closer to this site. Finally, a classifier built to discriminate between controls and stroke at the single-trial level can be used to generate an index of the disease state, the therapeutic score, which is validated on the group of rehabilitated mice. In conclusion, task-related neural activity can be used as an indicator of disease state and track recovery without selecting a peculiar feature of the neural responses. This novel method can be used in both the development and assessment of different therapeutic strategies.