Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of Elevated Plasma Total Homocysteine With Dementia With Lewy Bodies: A Case-Control Study

Background: Elevated plasma total homocysteine (tHcy) level, a known risk factor for vascular disease, is reported to be an independent risk factor for cognitive impairment and Alzheimer’s disease (AD) in most studies. tHcy may also be associated with dementia with Lewy bodies (DLB). Objective: To investigate the association between plasma tHcy levels and DLB or AD. Methods: This is a case-control study including 132 DLB patients, 264 AD patients, and 295 age-matched healthy controls. We used multivariate logistic regression model to analyze the data with adjustments for confounding variables. Results: The highest tHcy tertile (>13.9 μmol/L) was significantly independently associated with DLB [adjusted odds ratio (OR): 4.65, 95% confidence interval (CI): 1.95–11.10, P = 0.001] and AD (adjusted OR: 1.82, 95% CI: 1.02–3.23, P = 0.041) compared to the lowest tertile (<10.7 μmol/L). The cumulative frequency plots showed a shift in the distribution of the tHcy concentrations to higher values in patients with DLB compared to AD. The mean tHcy levels were stable and not altered by the duration of cognitive impairment prior to the collection of blood samples from DLB patients. Conclusion: Elevated plasma tHcy levels were independently associated with DLB, and the association was stronger for DLB than for AD. The lack of a relationship between tHcy levels and symptom duration may refute these observed associations being a consequence of DLB, and future longitudinal studies will be required to confirm whether tHcy plays a causative role in DLB.
A Putative C2H2 Transcription Factor CgTF6, Controlled by CgTF1, Negatively Regulates Chaetoglobosin A Biosynthesis in Chaetomium globosum

Gα signaling pathway as well as the global regulator LaeA were demonstrated to positively regulate the biosynthesis of chaetoglobosin A (ChA), a promising biotic pesticide produced by Chaetomium globosum. Recently, the regulatory function of Zn2Cys6 binuclear finger transcription factor CgcheR that lies within the ChA biosynthesis gene cluster has been confirmed. However, CgcheR was not merely a pathway specific regulator. In this study, we showed that the homologs gene of CgcheR (designated as Cgtf1) regulate ChA biosynthesis and sporulation in C. globosum NK102. More importantly, RNA-seq profiling demonstrated that 1,388 genes were significant differentially expressed as Cgtf1 deleted. Among them, a putative C2H2 transcription factor, named Cgtf6, showed the highest gene expression variation in zinc-binding proteins encoding genes as Cgtf1 deleted. qRT-PCR analysis confirmed that expression of Cgtf6 was significantly reduced in CgTF1 null mutants. Whereas, deletion of Cgtf6 resulted in the transcriptional activation and consequent increase in the expression of ChA biosynthesis gene cluster and ChA production in C. globosum. These data suggested that CgTF6 probably acted as an end product feedback effector, and interacted with CgTF1 to maintain a tolerable concentration of ChA for cell survival.
Long-Term Effects of Pediatric Acute Lymphoblastic Leukemia Chemotherapy: Can Recent Findings Inform Old Strategies?

During the last few decades, pediatric acute lymphoblastic leukemia (ALL) cure rates have improved significantly with rates exceeding 90%. Parallel to this remarkable improvement, there has been mounting interest in the long-term health of the survivors. Consequently, modified treatment protocols have been developed and resulted in the reduction of many adverse long-term consequences. Nevertheless, these are still substantial concerns that warrant further mitigation efforts. In the current review, pediatric-ALL survivors’ late adverse events, including secondary malignant neoplasms (SMNs), cardiac toxicity, neurotoxicity, bone toxicity, hepatic dysfunction, visual changes, obesity, impact on fertility, and neurocognitive effects have been evaluated. Throughout this review, we attempted to answer a fundamental question: can the recent molecular findings mitigate pediatric-ALL chemotherapy’s long-term sequelae on adult survivors? For SMNs, few genetic predisposition factors have been identified including TP53 and POT1 variants. Other treatment-related risk factors have been identified such as anthracyclines’ possible association with breast cancer in female survivors. Cardiotoxicity is another significant and common adverse event with some germline variants been found, albeit with conflicting evidence, to increase the risk of cardiac toxicity. For peripheral neurotoxicity, vincristine is the primary neurotoxic agent in ALL regimens. Some germline genetic variants were found to be associated with the vincristine neurotoxic effect’s vulnerability. However, these were mainly detected with acute neuropathy. Moreover, the high steroid doses and prolonged use increase bone toxicity and obesity risk with some pharmacogenetic biomarkers were associated with increased steroid sensitivity. Therefore, the role of these biomarkers in tailoring steroid choice and dose is a promising research area. Future directions in pediatric ALL treatment should consider the various opportunities provided by genomic medicine. Understanding the molecular bases underlying toxicities will classify patients into risk groups and implement a closer follow-up to those at higher risk. Pharmacogenetic-guided dosing and selecting between alternative agents have proven their efficacy in the short-term management of childhood ALL. It is the right time to think about a similar approach for the life-long consequences on survivors.
Variation in Onset of Leaf Unfolding and Wood Formation in a Central African Tropical Tree Species

A diversity of phenological strategies has been reported for tropical tree species. Defoliation and seasonal dormancy of cambial activity inform us on how trees cope with water stress during the dry season, or maximize the use of resources during the rainy season. Here, we study the matching between leaf phenology (unfolding and shedding) and cambial activity for Prioria balsamifera, a key timber species in the Democratic Republic of Congo. In particular, we (i) evaluated the seasonality of cambial activity and synchrony of phenology among trees in response to climate and (ii) identified the seasonality of leaf phenology and its relation with cambial phenology. The study was conducted in the Luki Man and Biosphere Reserve, located in the Mayombe forest at the southern margin of the Congo Basin. Historic defoliation data were collected every ten days using weekly crown observations whereas recent observations involved time-lapse cameras. Cambial pinning was performed on ten trees during 20 months and radius dendrometers were installed on three trees during 13 months. Tree rings were measured on cores from 13 trees and growth synchrony was evaluated. We found that P. balsamifera defoliates annually with a peak observed at the end of the dry season and the beginning of the rainy season. The new leaves unfolded shortly after shedding of the old leaves. The peak defoliation dates varied across years from September 12 to November 14 and the fraction of number of trees that defoliated at a given time was found to be negatively correlated with annual rainfall and temperature; during the dry season, when precipitation and temperatures are the lowest. Wood formation (radial growth), was found to be highly seasonal, with cambial dormancy occurring during the dry season and growth starting at the beginning of the rainy season. Individual ring-width series did not cross date well. The within species variability of leaf phenology and cambial rhythms provides indication about resistance of the population against climatic changes.
Reward Expectation Differentially Modulates Global and Local Spatial Working Memory Accuracy

Although it has been suggested that reward expectation affects the performance of spatial working memory tasks, controversial results have been found in previous experiments. Hence, it is still unclear to what extent reward expectation has an effect on working memory. To clarify this question, a memory-guided saccade task was applied, in which participants were instructed to retain and reconstruct a temporospatial sequence of four locations by moving their eyes in each trial. The global- and local-level spatial working memory accuracies were calculated to determine the reward effect on the global and local level of processing in spatial working memory tasks. Although high reward expectation enhanced the encoding of spatial information, the percentage of trials in which the cued location was correctly fixated decreased with increment of reward expectation. The reconstruction of the global temporospatial sequence was enhanced by reward expectation, whereas the local reconstruction performance was not affected by reward. Furthermore, the improvements in local representations of uncued locations and local sequences were at the cost of the representation of cued locations. The results suggest that the reward effect on spatial working memory is modulated by the level of processing, which supports the flexible resource theory during maintenance.
Proper Immune Response Depends on Early Exposure to Gut Microbiota in Broiler Chicks

The successional changes in the early intestinal microbiota occur concomitantly with the development, expansion, and education of the mucosal immune system. Although great attention of researchers has been focused on understanding the linkage between microbiota and immune functions, many essential details of the symbiotic relationship between the intestinal pioneer microbiota and the avian immune system remain to be discovered. This study was conducted to understand the impact of different early life intestinal colonizers on innate and adaptive immune processes in chicks and further identify immune-associated proteins expressed in the intestinal tissue. To accomplish it, we performed an in ovo application of two apathogenic Enterobacteriaceae isolates and lactic acid bacteria (L) to determine their influences on the intestinal proteome profile of broilers at the day of hatch (DOH) and at 10 days old. The results indicated that there were predicted biological functions of L-treated chicks associated with the activation and balanced function of the innate and adaptive immune systems. At the same time, the Enterobacteriaceae-exposed birds presented dysregulated immunological mechanisms or downregulated processes related to immune development. Those findings suggested that a proper immune function was dependent on specific gut microbiota exposure, in which the prenatal probiotic application may have favored the fitting programming of immune functions in chicks.
Remote-Sensing-Combined Haplotype Analysis Using Multi-Parental Advanced Generation Inter-Cross Lines Reveals Phenology QTLs for Canopy Height in Rice

High-throughput phenotyping systems with unmanned aerial vehicles (UAVs) enable observation of crop lines in the field. In this study, we show the ability of time-course monitoring of canopy height (CH) to identify quantitative trait loci (QTLs) and to characterise their pleiotropic effect on various traits. We generated a digital surface model from low-altitude UAV-captured colour digital images and investigated CH data of rice multi-parental advanced generation inter-cross (MAGIC) lines from tillering and heading to maturation. Genome-wide association studies (GWASs) using the CH data and haplotype information of the MAGIC lines revealed 11 QTLs for CH. Each QTL showed haplotype effects on different features of CH such as stage-specificity and constancy. Haplotype analysis revealed relationships at the QTL level between CH and, vegetation fraction and leaf colour [derived from UAV red–green–blue (RGB) data], and CH and yield-related traits. Noticeably, haplotypes with canopy lowering effects at qCH1-4, qCH2, and qCH10-2 increased the ratio of panicle weight to leaf and stem weight, suggesting biomass allocation to grain yield or others through growth regulation of CH. Allele mining using gene information with eight founders of the MAGIC lines revealed the possibility that qCH1-4 contains multiple alleles of semi-dwarf 1 (sd1), the IR-8 allele of which significantly contributed to the “green revolution” in rice. This use of remote-sensing-derived phenotyping data into genetics using the MAGIC lines gives insight into how rice plants grow, develop, and produce grains in phenology and provides information on effective haplotypes for breeding with ideal plant architecture and grain yield.
Extensive Anti-CoA Immunostaining in Alzheimer’s Disease and Covalent Modification of Tau by a Key Cellular Metabolite Coenzyme A

Alzheimer’s disease (AD) is a neurodegenerative disorder, accounting for at least two-thirds of dementia cases. A combination of genetic, epigenetic and environmental triggers is widely accepted to be responsible for the onset and development of AD. Accumulating evidence shows that oxidative stress and dysregulation of energy metabolism play an important role in AD pathogenesis, leading to neuronal dysfunction and death. Redox-induced protein modifications have been reported in the brain of AD patients, indicating excessive oxidative damage. Coenzyme A (CoA) is essential for diverse metabolic pathways, regulation of gene expression and biosynthesis of neurotransmitters. Dysregulation of CoA biosynthesis in animal models and inborn mutations in human genes involved in the CoA biosynthetic pathway have been associated with neurodegeneration. Recent studies have uncovered the antioxidant function of CoA, involving covalent protein modification by this cofactor (CoAlation) in cellular response to oxidative or metabolic stress. Protein CoAlation has been shown to both modulate the activity of modified proteins and protect cysteine residues from irreversible overoxidation. In this study, immunohistochemistry analysis with highly specific anti-CoA monoclonal antibody was used to reveal protein CoAlation across numerous neurodegenerative diseases, which appeared particularly frequent in AD. Furthermore, protein CoAlation consistently co-localized with tau-positive neurofibrillary tangles, underpinning one of the key pathological hallmarks of AD. Double immunihistochemical staining with tau and CoA antibodies in AD brain tissue revealed co-localization of the two immunoreactive signals. Further, recombinant 2N3R and 2N4R tau isoforms were found to be CoAlated in vitro and the site of CoAlation mapped by mass spectrometry to conserved cysteine 322, located in the microtubule binding region. We also report the reversible H2O2-induced dimerization of recombinant 2N3R, which is inhibited by CoAlation. Moreover, CoAlation of transiently expressed 2N4R tau was observed in diamide-treated HEK293/Pank1β cells. Taken together, this study demonstrates for the first time extensive anti-CoA immunoreactivity in AD brain samples, which occurs in structures resembling neurofibrillary tangles and neuropil threads. Covalent modification of recombinant tau at cysteine 322 suggests that CoAlation may play an important role in protecting redox-sensitive tau cysteine from irreversible overoxidation and may modulate its acetyltransferase activity and functional interactions.
Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality

Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.
Advanced Fusion and Empirical Mode Decomposition-Based Filtering Methods for Breathing Rate Estimation from Seismocardiogram Signals

Breathing Rate (BR), an important deterioration indicator, has been widely neglected in hospitals due to the requirement of invasive procedures and the need for skilled nurses to be measured. On the other hand, biomedical signals such as Seismocardiography (SCG), which measures heart vibrations transmitted to the chest-wall, can be used as a non-invasive technique to estimate the BR. This makes SCG signals a highly appealing way for estimating the BR. As such, this work proposes three novel methods for extracting the BR from SCG signals. The first method is based on extracting respiration-dependent features such as the fundamental heart sound components, S1 and S2 from the SCG signal. The second novel method investigates for the first time the use of data driven methods such as the Empirical Mode Decomposition (EMD) method to identify the respiratory component from an SCG signal. Finally, the third advanced method is based on fusing frequency information from the respiration signals that result from the aforementioned proposed methods and other standard methods. The developed methods in this paper are then evaluated on adult recordings from the combined measurement of ECG, the Breathing and Seismocardiograms database. Both fusion and EMD filter-based methods outperformed the individual methods, giving a mean absolute error of 1.5 breaths per minute, using a one-minute window of data.
Routing Methods for Mobile Ad-hoc Network: A Review and Comparison of Multi-criteria Approaches

In recent years, Mobile Ad-hoc Networks have been focused on research and strong applications in healthcare, military, disaster prevention, and IoT ecosystem. Due to the ad-hoc mobility characteristic of the network devices, the routing protocols are specifically designed to ensure factors such as energy efficiency, high performance, quality of service, as well as security-aware. In this article, we perform analytic routing protocols for mobile ad hoc networks to compare and evaluate the advantages and disadvantages of each protocol and propose the next research direction.
E�cient in vitro plant regeneration from leaf derived callus and genetic �delity assessment of an endemic medicinal plant of Ranunculus wallichianus Wight & Arnn using RAPD and ISSR markers

Ranunculus wallichianus is a medicinally important plant and an endemic species to Western Ghats of South India. An e�cient and reliable indirect regeneration protocol system for R. wallichianus was developed from leaf explants in the present investigation. Leaf explants were cultured on both full-strength and half-strength MS (Murashige & Skoog) medium supplemented with different concentrations (1.0 mg L − 1 to 3.0 mg L − 1 ) of 2,4-D and NAA. Among the different concentrations tested, the highest percentage of yellowish green compact nodular callus formation was observed on half-strength MS medium with 2.0 mg L − 1 of 2, 4-D. Then, the in vitro raised organogenic callus was cultured on half strength MS medium containing various concentrations (1.0 mg L − 1 to 3.0 mg L − 1 ) of BA, KIN and TDZ with 0.5 mg L − 1 NAA and 10% CW for in vitro shoot regeneration. The highest percentage of regeneration response (97%) and maximum number of shoots formation (11.1 ± 0.13 shoots/culture with 9.2 ± 0.35 cm mean shoot length) were obtained from MS medium containing 2.5 mg L − 1 BA with 0.5 mg L − 1 NAA and 10% CW. The well elongated in vitro raised shoots were rooted in half strength MS medium with 2.5 mg L − 1 IBA + 250 mg L − 1 activated charcoal shows high frequency of root formation. The well rooted plantlets were successfully hardened and acclimatized with the survival rate of 94%. Clonal �delity of in vitro raised plantlets was assessed by using DNA based RAPD and ISSR molecular markers. The total of 56 and 47 monomorphic bands were obtained from RAPD and ISSR markers respectively. This present in vitro propagation protocol system could be an effective for the conservation of R. wallichianus with their genetic purity and its further investigations.
ERP-DDA: Event Reporting Protocol Based on Distributed Data Aggregation for Wireless Sensor Networks

Wireless Sensor Networks (WSNs) have a wide range of applications in human life. Accordingly, WSNs have beenthoroughly considered in research community to improve their performance and address their challenges. Eventreporting in WSNs has always been a major challenge in terms of energy consumption. Event reporting requiressensing the event and sending a reporting packet from the sensor to the centralized base station (BS). However,sensor’s energy is limited and stored in a non-rechargeable battery. Therefore, several event-reporting (or datacollection) protocols have been proposed to improve energy consumption in WSNs, and consequently, to extendtheir lifetime. In this paper, we propose an efficient event reporting protocol for WSNs called Event ReportingProtocol Based on Distributed Data Aggregation (ERP-DDA). This protocol mainly aims at reporting any event byno more than one sensor node such that energy saving is satisfied in the whole network. To achieve this goal, ERPDDAis mainly based on the following features: it is a cluster-based protocol, it is a multi-hop routing protocol, itapplies distributed data aggregation, and it employs variable clustering and cluster head selection. Simulationsshow that ERP-DDA significantly extends the lifetime of WSNs compared with other related protocols.