Miracle-dz/UniFAR-FTUs huggingface dataset:
TEclass2: Classification of transposable elements using Transformers

Motivation Transposable elements (TEs) are interspersed repetitive sequences that are major constituents of most eukaryotic genomes and are crucial for genome evolution. Despite the existence of multiple tools for their classification and annotation, none of them can achieve completely reliable results making it a challenge for genomic studies. In this work, we introduce TEclass2, a new software that uses a deep learning approach based upon a linear Transformer architecture with a k-mer to-kenizer and further adaptations to handle DNA sequences. This software has an easy configuration that allows training models on new datasets and the classification of TE models providing multiple metrics for a reliable evaluation of the results. Results This work shows a successful adaptation of deep learning with Transformers for the classification of TE models from consensus sequences, and these results lay a foundation for novel methodologies in bioinformatics. We provide a tool for the training of models and the classification of consensus sequences from TE models on custom data and a web page interface with a pre-trained dataset based on curated and non-curated TE libraries allowing a fast and simple classification of TEs. Availability https://bioinformatics.uni-muenster.de/tools/teclass2/index.pl Contact wojmak@uni-muenster.de Supplementary information Supplementary data are available at Bioinformatics online.
Fine-grained descending control of steering in walking Drosophila

Locomotion involves rhythmic limb movement patterns that originate in circuits outside the brain. Purposeful locomotion requires descending commands from the brain, but we do not understand how these commands are structured. Here we investigate this issue, focusing on the control of steering in walking Drosophila. First, we describe different limb “gestures” associated with different steering maneuvers. Next, we identify a set of descending neurons whose activity predicts steering. Focusing on two descending cell types downstream from distinct brain networks, we show that they evoke specific limb gestures: one lengthens strides on the outside of a turn, while the other attenuates strides on the inside of a turn. Notably, a single descending neuron can have opposite effects during different locomotor rhythm phases, and we identify networks positioned to implement this phase-specific gating. Together, our results show how purposeful locomotion emerges from brain cells that drive specific, coordinated modulations of low-level patterns.
Constrained optimization of a newsboy problem with return policy

A newsboy model in which a vendor has a limited budget to procure the required items is developed. It is assumed that the manufacturer will either sell the items to the vendor outright or offer the items to the vendor with return policy. In the latter case, the manufacturer buys back from the vendor the unsold items at the end of the selling season. This study considers one item with budget constraints. The vendor has the option of purchasing the goods outright, obtaining the goods with return policy, or a combination of both. By using Kuhn-Tucker Conditions and inductive method, our analysis proposes an optimal inventory policy theorem. The purpose of this study is to investigate how the vendor should replenish the items with return policy under limited budget and changing prices. We show that there exists a set of conditions under which the vendor's optimal strategy will change based on the amount of available budget for product procurement. If the purchase price with return policy is greater than the price of outright purchase and the vendor has a small amount of available budget, only outright purchase will be optimal. However, if the budget reaches a certain threshold amount, mixed strategies where items are obtained by outright purchase and with return policy are used. We also show that when the purchase price with return policy is not greater than the outright purchase, the vendor will only obtain the items with return policy.
Longitudinal observations of the effects of ischemic stroke on binaural perception

Acute ischemic stroke, characterized by a localized reduction in blood flow to specific areas of the brain, has been shown to affect binaural auditory perception. In a previous study conducted during the acute phase of ischemic stroke, two tasks of binaural hearing were performed: binaural tone-in-noise detection, and lateralization of stimuli with interaural time- or level differences (Dietze et al., 2022, Front. Neurosci. 16:1022354). Various lesion-specific, as well as individual, differences in binaural performance between patients in the acute phase of stroke and a control group were demonstrated. For the current study, we re-invited the same group of patients, whereupon a subgroup repeated the experiments during the subacute and chronic phases of stroke. Similar to the initial study, this subgroup consisted of patients with lesions in different locations, including cortical and subcortical areas. At the group level, the results from the tone-in-noise detection experiment remained consistent across the three measurement phases, as did the number of deviations from normal performance in the lateralization task. However, the performance in the lateralization task exhibited variations over time among individual patients. Some patients demonstrated improvements in their lateralization abilities, indicating recovery, whereas others’ lateralization performance deteriorated during the later stages of stroke. Notably, our analyses did not reveal consistent patterns for patients with similar lesion locations. These findings suggest that recovery processes are more individual than the acute effects of stroke on binaural perception. Individual impairments in binaural hearing abilities after the acute phase of ischemic stroke have been demonstrated and should therefore also be targeted in rehabilitation programs.
Network analyses reveal D clade ethylene response factors as major regulators of jasmonic acid-mediated resistance to early blight disease complex in tomato

Resistance mechanisms to early blight disease complex (EBDC) in tomato remain obscure given its polygenic and quantitative nature. We investigated the early defense responses of Heinz 1706 tomato to EBDC using RNA-seq. We observed distinct transcriptional reprofiling upon exposure to two EBDC isolates and the PAMP chitin. Avirulent isolate CS046 (Alternaria alternata) elicited a vigorous defense response in the host, whilst the virulent isolate 1117-1 (Alternaria sect. Porri) showed subdued gene expression, suggesting a suppression of defense responses during compatible pathogenesis. We emphasize the specific roles of ETHYLENE RESPONSE FACTORs (ERFs) in defense against EBDC, with a particular focus on the D clade ERFs. Co-expression network analysis revealed the principal genes in early defense responses to EBDC are secondary metabolite biosynthesis genes, transcription factors, and hormone response genes. We constructed a gene regulatory network and predicted novel hub genes as putative global regulators of the defense response, including the D clade ERFs, WRKY, and NAC transcription factors. Our work highlights the failure of virulent EBDC pathogenesis to elicit hormone responses that suppress cell death. Additionally, we found a selective induction for specific ERFs that strongly influence the topology of the EBDC defense transcriptional network.
A Review of Lake Bonneville Shoreline Faunas (Late Pleistocene) of Northern Utah

Abstract Lake Bonneville is the most studied pluvial lake in North America. At its highest stand in the late Pleistocene, the lake inundated several thousand square kilometers of western Utah, extreme eastern Nevada and Southern Idaho. The mammalian fauna collected from the shoreline deposits of the lake is composed of a diverse late Pleistocene (Rancholabrean NALM A) assemblage. There are at least 15 large mammalian taxa recognized of which ten are extinct (Arctodus simus, Equus sp., Platygonus compressus, Camelops hesternus, Bison bison subsp., Navahoceros sp., Symbos cavifrons, Bootherium bombifrons, Mammut americanum, Mammuthus columbi), one locally extirpated (Canis lupus) and four are extant (Vulpes vulpes, Ursus americanus, Ovis canadensis, Odocoileus hemionus). Most fossils have been collected from the commercial sand and gravel quarries that line the Wasatch and Oquirrh Mountain fronts. All specimens are believed to be associated with the final rise and fall of Lake Bonneville (Bonneville Lake Cycle). The mammals seem to be indicative of open park lands or grasslands situated in coniferous forests.
Early secretory antigen target of 6-kDa of Mycobacterium tuberculosis inhibits macrophage apoptosis and host defense via TLR2

Mycobacterium tuberculosis (M. tuberculosis) is an intracellular bacteria capable of evading the human immune system through various mechanisms. M. tuberculosis secretes many virulence factors when infecting host cells. The 6 kDa early secretory antigen target (ESAT-6) is one of the most virulent factors producted by the ESX-1 system, which acts alone or in conjunction with culture ﬁltrate protein 10 (CFP-10) to involve in host-pathogen interactions. ESAT-6 has been widely investigated in M. tuberculosis pathogenicity and vaccination. Nonetheless, little is known about its contribution to M. tuberculosis immune evasion and the involved cellular mechanisms. In this study, diﬀerential genes between BCG with the region of diﬀerence-1 (RD1) gene and Bacille Calmette-Gu´erin (BCG) infected dendritic cells (DC) were analyzed to reveal that ESAT-6, expressed in the RD1 region, involves host denfensive function of DC in response to BCG. In vitro evidence indicated that ESAT-6 (5 μ g/ml) inhibits M. tuberculosis-induced apoptosis in THP-1(A) macrophages by suppressing TLR2 and via caspase-9 and caspase-3 endogenous pathways. It also inhibits the expression of IL-10, TNF-α, IL-12, and the phagocytosis of macrophages. Additionally, ESAT-6 suppresses the bactericidal activity of macrophages, including ROS production, and the killing of M. tuberculosis. In summary, these data suggest a central role of ESAT-6 in M. tuberculosis’s evasion from macrophage recognition, phagocytosis, killing, and apoptosis. Our work may provide a theoretical basis for exploring new molecular targets of M. tuberculosis both for innovative vaccines and therapeutic inventions.
LSU Scholarly

HMGB proteins are eukaryotic, chromatin-associated proteins that play roles in both DNA dynamics and transcription regulation. Hmo1p is an HMGB protein in Saccharomyces cerevisiae that behaves somewhat like a hybrid between mammalian HMGB proteins and the metazoan linker histone H1. mTORC1, a protein complex containing the Tor1p kinase and a major regulator of cellular growth, is inhibited by both rapamycin and stress. It has also been shown to not only associate with Hmo1p at various gene promoters, but also regulate the HMO1 gene itself through direct binding. In this study, the Hmo1p-mTORC1 relationship was further investigated through two questions: 1) Does the transcription factor Sfp1p play a role in relaying mTORC1’s signal to the HMO1 promoter, and 2) Is the reduction in HMO1 transcripts during stress dependent on mTORC1? Gene expression analyses revealed that Sfp1p is not required for normal HMO1 transcription; however, it does appear to play a role in transmitting the mTORC1 stress signal to the promoter, as transcripts are only significantly decreased during stress when Sfp1p is present. Survival tests revealed that Sfp1p might be hindering the cell’s ability to repair DNA double-strand breaks, as there is a slight increase in cell survival during double-strand break-induction when Sfp1p is knocked-out; however, there is some uncertainty as to whether this is Hmo1p-related. Chromatin Immunoprecipitation techniques were then used to demonstrate that RNA polymerase II is evicted from the HMO1 gene over the course of one hour during stress when Tor1p is knocked-out. This same phenomenon had previously been shown in wild-type cells; however, HMO1 transcripts are only attenuated in wild-type cells, and not when Tor1p is knocked-out. This suggests that mTORC1 is responsible for the reduction of HMO1 mRNA during stress.
Magnetic Resonance Imaging in Huntington Disease

Huntington disease is a progressive neurodegenerative disorder characterized by movement disorder, progressive dementia, and emotional disturbances. Morphologically it is characterized by diffuse atrophy, with the greatest loss of neurons seen in the caudate nucleus and putamen. The basal ganglia at death weigh about 50% of normal [1] and also demonstrate neuronal loss and gliosis. Receptor binding studies of postmortem specimens suggest that certain intrinsic striatal neurons and their efferent pathways to globus pallid us and substantia nigra are the major sites of pathologic disruption [2]. The pneumoencephalographic [3,] , CT [4, 5], and pOSitron emission 18FDG findings [6] in Huntington disease have been described. We describe the magnetic resonance (MR) findings in four patients with known Huntington disease.
Scientific Journal of Applied Social and Clinical Science

: In recent years, the development of sustainable tourism has become a major challenge for tourist destinations.One of the types of tourism that generates the greatest problems of mass tourism is cruise tourism, given the large number of people who disembark at a port of call to visit the destination. However, the study of the perception of overcrowding from the point of view of the cruise passenger is still scarce, requiring further research in this area. For this reason, and based on a sample of cruise passengers, this paper analyzes the perception of tourist massification that this tourist has and its influence on post-visit behavior. The results indicate that the perception of overcrowding is moderate, not directly influencing their post-visit intentions. The results suggest relevant implications for destination tourism managers.
CLASS IMBALANCE LEARNING WITH COSTSENSITIVE-ACGAN

The class imbalance problem has been recognized in many real-world applications and negatively affects machine learning performance. Generative Adversarial Networks or GANs have been known to be the next best thing in image generation. However, most GANs do not consider classes and when they do, cannot perform well under the imbalance problem. Based on related works, the modification of the loss function and various resampling methods have been commonly applied to counter the problem of class imbalance. In this study, CostSensitive-ACGAN is introduced which is a variation of Auxiliary Classifier GAN (ACGAN) that can work better under the class imbalance condition. This method incorporated the idea of applying cost-sensitive learning in the loss function to further improve the classification of minority classes. Cost-sensitive parameters are determined adaptively according to the classification error of the class to improve minority classes presence. By applying higher misclassification costs for minority classes, these instances can be magnified and recognized by the discriminator thus improving image generation altogether. This method has shown comparatively competitive results with existing benchmark models.
Simulation of dust aerosol and its regional feedbacks over East Asia using a regional climate model

Abstract. The ICTP regional climate model (RegCM3) coupled with a desert dust aerosol model is used to simulate the net radiative forcing (short-wave and long-wave) and related climate effects of dust aerosols over East Asia. Two sets of experiments are completed and intercompared, one without (Exp. 1) and one with (Exp. 2) the radiative effects of dust aerosols. The experiments encompass the main dust producing months, February through May, for 10 years (1997–2006), and the simulation results are evaluated against ground station and satellite data. The model captures the basic observed climatology over the area of interest. The spatial and temporal variations of near surface concentration, mass load, optical depth and emission of dust aerosols from the main source regions are reproduced by model. The main model deficiency is an overestimate of dust amounts over the source regions and an underestimate downwind of these source areas, which indicates an underestimate of dust dispersal. Over the desert source regions, the net TOA radiative forcing is positive, while it is small over the other regions as a result of high surface albedo values which reduce the short-wave radiative forcing. The net surface radiative fluxes are decreased by dust and this causes a surface cooling locally up to −1°C. The inclusion of net (short-wave and long-wave) dust radiative forcing leads to a reduction of dust emission in the East Asia source regions, which is mainly caused by an increase in local stability and a corresponding decrease in dust lifting. Our results indicate that dust effects should be included in the assessment of climate change over East Asia.
Suckling piglets submitted to creep feeding management from 5 days-old showed optimal performance and exploratory behaviour

This study aimed to assess the effects of starting creep feeding at different ages on performance, behaviour, haematological, and biochemical parameters in piglets. A total of 138 piglets (1.34 ± 0.25 kg, n = 13 sows), weaned at 21 d-old, were assigned to treatments using a completely randomized design. The litter was divided into two groups: seven litters (n = 80 piglets) were subjected to creep feeding on the fifth day of age (creep 5) and five litters (n = 58 piglets), on the tenth day of age (creep 10). Piglets were weighed at birth, weaning, and after the first week in the nursery. Piglet behaviour was evaluated daily for 15 min until day 20. Blood was collected on day 13, at weaning, and at the end of the first week in the nursery. There was no difference in body weight in the suckling phase, but piglets fed Creep 5 showed greater body weight gain in the first nursery week. The Creep 5 group had lower feed leftovers during the five days of evaluation of feed intake. There were no differences in haematological parameters and amylase concentration; however, the piglets spent more time lying down, sucking, and massaging the udder. On day 8, the piglets in the Creep 5 group showed a higher frequency of exploratory behaviour. In conclusion, piglets fed Creep 5 had optimal performance after weaning and improved feed intake capacity by displaying more exploratory behaviour than Creep 10. Creep management did not alter haematological and biochemical parameters.
Rationales in Old World Base Glass Compositions

Abstract It is long known that most Egyptian and Roman base glass compositions show a remarkably small scatter in their chemical composition. By plotting appropriately reduced base glass compositions in ternary phase diagrams it is demonstrated that the compositional fields defined by the compositional scatter are closely related to eutectic regions within the relevant phase diagrams. This is interpreted as to be due to an eutectic melting regime, i.e. partial melting in the presence of a crystalline buffer or residuum, and not primarily a result of strict recipe and raw material control. Furthermore, it is demonstrated that possibly two independent melting temperature indicators are correlated, suggesting a factual relationship between melting temperature and melt composition. This evidence is taken to develop a “partial batch melting model” for these early glasses, as opposed to the “total batch melting model” of Mediaeval and early modern glasses. Some archaeological implications of this model are briefly discussed.
Organic Agriculture in Egypt: Production Economics and Challenges (A Case Study of Fayoum Governorate)

The organic agriculture is no more a phenomenon of developed countries. The organic agriculture is revolutionary hitting the agriculture sector in Egypt. Fayoum governorate is considered the third between the Egyptian governorates with regard to the organic agricultural land and many researchers considered developing research about. The profitability of organic production is high when targeting international markets as the awareness of using organic products in Egypt is still in progress. Years of experience, area cultivated, and the growing method are constraints for the productivity per feddan of the organic production. Enas E. Sadek and Ayman A. Shelaby. Organic Agriculture in Egypt: Production Economics and Challenges (A Case Study of Fayoum Governorate). Journal of American Science 2011; 7(9):208-215). (ISSN: 1545-1003). http://www.americanscience. org .
Calibration of Mean Wind Proﬁles Using Wind Lidar Measurements

: This paper explores the applicability of Lidar wind measurements for the calibration of mean wind proﬁles depending on the extension in time and space of the available measurements. Starting from logarithmic wind speed proﬁles corresponding to different site conditions, pseudo-experimental wind speed proﬁles are generated artiﬁcially by adding a zero-mean Gaussian-distributed noise, representative of realistic measurement errors. Then, a least-square ﬁtting procedure is applied to identify the roughness length and the zero-plane displacement. The results obtained show an increase in the scatter of the estimated parameters of the logarithmic law with increasing elevation of the lowest measurement point. Then, a parametric study is developed to analyse the inﬂuence of the number of available experimental proﬁles on the uncertainty associated with the estimated logarithmic law parameters. Based on the results obtained, it can be pointed out that the availability of measurements at low elevations is essential to identify the logarithmic mean wind proﬁle using a reasonable number of observations.
Changes in Duration-Related Characteristics of Late-Summer Precipitation over Eastern China in the Past 40 Years

AbstractDuration is a key feature of rainfall events that is closely related to rainfall mechanisms and influences. This study analyzes the decadal change in the duration-related characteristics of late-summer (July–August) precipitation over eastern China during 1966–2005. Accompanying the southern-flooding and northern-drought (SFND) pattern of rainfall amount over the eastern China in recent decades, the duration-related rainfall structure also experienced significant changes. In North China, the frequency of short duration rainfall events decreased and their intensity increased. The decadal decreases of rainfall amount over North China are largely contributed by long duration rainfall events, especially those occurring between midnight and morning. In the mid-to-lower reaches of the Yangtze River valley, both the frequency and amount of long duration precipitation have significantly increased. The mean and maximum duration time of late-summer precipitation has increased 0.85 and 7.61 h, respectively.