Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive Segmentation Techniques for Efficient Representation of Time Series Datasets. (Techniques de segmentation adaptative pour une représentation efficace des séries temporelles)

Many applications in different domains generate time series data at an increasing rate. The continuous flow of emitted data may concern personal activities (e.g., through smart-meters or smart-plugs for electricity or water consumption) or professional activities (e.g., for monitoring heart activity or through the sensors installed on plants by farmers). This results in the production of large and complex data, usually in the form of time series. In recent years, there has been an explosion of interest in time series data mining. As a general rule, large time series come along with super-high dimensionality. As a consequence, it is difficult and inefficient to directly mine the raw time series without relying on dimensionality reduction. Therefore, the representation of the data is the key to efficient and effective solutions. Given this high data volumes in time series applications, or simply the need for fast response times, it is necessary to rely on alternative, shorter representations of these series, usually with loss. This incurs approximate comparisons of time series where precision is a major issue. In this thesis, we focus on the problem of segmenting time series before their transformation into symbolic representations. For this, we propose solutions to adaptively segment time series databases by adopting a variable segment size that depends on the time series distribution. These methods reduce significantly the information loss incurred by possible splittings at different steps of the representation calculation, particularly for datasets with unbalanced (non-uniform) distributions. After reviewing the state of the art, we propose three novel approaches for efficiently segmenting time series datasets by means of variable size segments. First, we propose ASAX_EN a novel approach that performs the splitting based on the representation’s entropy with an approximate algorithm using a top-down strategy. Second, we propose ASAX_SSE approach that segments the time series by taking into account the sum of squared errors (SSE) with an approximate algorithm using a bottom-up strategy. This method provides high quality results in time series representation. Also, efficient algorithms for improving the execution time of our segmentation approach have been proposed. Third, we propose EASAX_SSE our segmentation method that finds the time domain division that guarantees to minimize the SSE of the representation with an exact method. Our solutions propose a lower bounding method that allows approximating the distance between the original time series based on their representations in these approaches. They have been evaluated using several real world datasets. The results illustrate that our techniques can significantly improve the time series representation quality.
Factors affecting IgG4-mediated complement activation

Of the four human immunoglobulin G (IgG) subclasses, IgG4 is considered the least inflammatory, in part because it poorly activates the complement system. Regardless, in IgG4 related disease (IgG4-RD) and in autoimmune disorders with high levels of IgG4 autoantibodies, the presence of these antibodies has been linked to consumption and deposition of complement components. This apparent paradox suggests that conditions may exist, potentially reminiscent of in vivo deposits, that allow for complement activation by IgG4. Furthermore, it is currently unclear how variable glycosylation and Fab arm exchange may influence the ability of IgG4 to activate complement. Here, we used well-defined, glyco-engineered monoclonal preparations of IgG4 and determined their ability to activate complement in a controlled system. We show that IgG4 can activate complement only at high antigen and antibody concentrations, via the classical pathway. Moreover, elevated or reduced Fc galactosylation enhanced or diminished complement activation, respectively, with no apparent contribution from the lectin pathway. Fab glycans slightly reduced complement activation. Lastly, we show that bispecific, monovalent IgG4 resulting from Fab arm exchange is a less potent activator of complement than monospecific IgG4. Taken together, these results imply that involvement of IgG4-mediated complement activation in pathology is possible but unlikely.
Characterization of the soybean KRP gene family reveals a key role for GmKRP2a in root development

Kip-related proteins (KRPs), as inhibitory proteins of cyclin-dependent kinases, are involved in the growth and development of plants by regulating the activity of the CYC-CDK complex to control cell cycle progression. The KRP gene family has been identified in several plants, and several KRP proteins from Arabidopsis thaliana have been functionally characterized. However, there is little research on KRP genes in soybean, which is an economically important crop. In this study, we identified nine GmKRP genes in the Glycine max genome using HMM modeling and BLASTP searches. Protein subcellular localization and conserved motif analysis showed soybean KRP proteins located in the nucleus, and the C-terminal protein sequence was highly conserved. By investigating the expression patterns in various tissues, we found that all GmKRPs exhibited transcript abundance, while several showed tissue-specific expression patterns. By analyzing the promoter region, we found that light, low temperature, an anaerobic environment, and hormones-related cis-elements were abundant. In addition, we performed a co-expression analysis of the GmKRP gene family, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) set enrichment analysis. The co-expressing genes were mainly involved in RNA synthesis and modification and energy metabolism. Furthermore, the GmKRP2a gene, a member of the soybean KRP family, was cloned for further functional analysis. GmKRP2a is located in the nucleus and participates in root development by regulating cell cycle progression. RNA-seq results indicated that GmKRP2a is involved in cell cycle regulation through ribosome regulation, cell expansion, hormone response, stress response, and plant pathogen response pathways. To our knowledge, this is the first study to identify and characterize the KRP gene family in soybean.
Relationship between glycemic control and cognitive impairment: A systematic review and meta-analysis

Background Diabetes mellitus, or hyperglycemia, is an independent risk factor for cognitive impairment. Here we systematically analyzed whether glycemic control could improve cognitive impairment in patients with diabetes mellitus (DM), hyperglycemia, or insulin resistance. Methods Three databases (PubMed, EMBASE, and Cochrane Library) and ClinicalTrials.gov were searched for randomized controlled trials analyzing the relationship between glycemic control and cognitive function assessments, published from database inception to June 2022. Patients in experimental groups were treated with antidiabetic drugs, while control groups were treated with a placebo or alternative antidiabetic drugs. Data analysis was conducted using RevMan 5.3 and StataSE-64, and standardized mean difference (SMD) and 95% confidence intervals (CIs) were calculated. Results Thirteen studies comprising 19,314 participants were included. Analysis revealed that glycemic control significantly attenuated the degree of decline in cognitive function assessment scores (SMD = 0.15; 95% CI 0.05, 0.26; p < 0.00001), and funnel plots confirmed no publication bias. Seven studies used Mini-Mental State Examination as the primary cognitive function assessment, showing that glycemic control significantly delayed the degree of decline in cognitive function assessment scores (SMD = 0.18; 95% CI 0.03, 0.34; p = 0.02). Similar results were seen in two studies using the Montreal Cognitive Assessment scale, but without significant difference (SMD = 0.05; 95% CI-0.10, 0.21; p = 0.51). One study using Auditory Word Learning Test (AVLT) showed that glycemic control significantly delayed the decline in cognitive function assessment scores (SMD = 0.52; 95% CI 0.11,0.93; p = 0.01), and another used Wechsler Memory Scale Revised, showing similar results (SMD = 1.45; 95% CI 0.86, 2.04; p < 0.00001). Likewise, a study that used Modified Mini-Mental State scale showed that glycemic control significantly delayed the decline in cognitive function assessment scores (SMD = -0.10; 95% CI-0.16, −0.03; p = 0.005). Lastly, one study used AVLT subtests to show that glycemic control delayed the decline in cognitive function assessment scores, although not statistically significant (SMD = 0.09; 95% CI-0.53, 0.71; p = 0.78). Conclusion Glycemic control through antidiabetic treatment correlates with the improvement of cognitive impairment in patients with DM, hyperglycemia or insulin resistance. However, further studies are needed to validate the results of this study. Systematic Review Registration PROSPERO, identifier CRD42022342260.
Fpr2 exacerbates Streptococcus suis-induced streptococcal toxic shock-like syndrome via attenuation of neutrophil recruitment

The life-threatening disease streptococcal toxic shock-like syndrome (STSLS), caused by the bacterial pathogen Streptococcus suis (S. suis). Proinflammatory markers, bacterial load, granulocyte recruitment, and neutrophil extracellular traps (NETs) levels were monitored in wild-type (WT) and Fpr2-/- mice suffering from STSLS. LXA4 and AnxA1, anti-inflammatory mediators related to Fpr2, were used to identity a potential role of the Fpr2 in STSLS development. We also elucidated the function of Fpr2 at different infection sites by comparing the STSLS model with the S. suis-meningitis model. Compared with the WT mice, Fpr2-/- mice exhibited a reduced inflammatory response and bacterial load, and increased neutrophil recruitment. Pretreatment with AnxA1 or LXA4 impaired leukocyte recruitment and increased both bacterial load and inflammatory reactions in WT but not Fpr2-/- mice experiencing STSLS. These results indicated that Fpr2 impairs neutrophil recruitment during STSLS, and this impairment is enhanced by AnxA1 or LXA4. By comparing the functions of Fpr2 in different S. suis infection models, inflammation and NETs was found to hinder bacterial clearance in S. suis meningitis, and conversely accelerate bacterial clearance in STSLS. Therefore, interference with neutrophil recruitment could potentially be harnessed to develop new treatments for this infectious disease.
Network analyses of upper and lower airway transcriptomes identify shared mechanisms among children with recurrent wheezing and school-age asthma

Background Predicting which preschool children with recurrent wheezing (RW) will develop school-age asthma (SA) is difficult, highlighting the critical need to clarify the pathogenesis of RW and the mechanistic relationship between RW and SA. Despite shared environmental exposures and genetic determinants, RW and SA are usually studied in isolation. Based on network analysis of nasal and tracheal transcriptomes, we aimed to identify convergent transcriptomic mechanisms in RW and SA. Methods RNA-sequencing data from nasal and tracheal brushing samples were acquired from the Gene Expression Omnibus. Combined with single-cell transcriptome data, cell deconvolution was used to infer the composition of 18 cellular components within the airway. Consensus weighted gene co-expression network analysis was performed to identify consensus modules closely related to both RW and SA. Shared pathways underlying consensus modules between RW and SA were explored by enrichment analysis. Hub genes between RW and SA were identified using machine learning strategies and validated using external datasets and quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Finally, the potential value of hub genes in defining RW subsets was determined using nasal and tracheal transcriptome data. Results Co-expression network analysis revealed similarities in the transcriptional networks of RW and SA in the upper and lower airways. Cell deconvolution analysis revealed an increase in mast cell fraction but decrease in club cell fraction in both RW and SA airways compared to controls. Consensus network analysis identified two consensus modules highly associated with both RW and SA. Enrichment analysis of the two consensus modules indicated that fatty acid metabolism-related pathways were shared key signals between RW and SA. Furthermore, machine learning strategies identified five hub genes, i.e., CST1, CST2, CST4, POSTN, and NRTK2, with the up-regulated hub genes in RW and SA validated using three independent external datasets and qRT-PCR. The gene signatures of the five hub genes could potentially be used to determine type 2 (T2)-high and T2-low subsets in preschoolers with RW. Conclusions These findings improve our understanding of the molecular pathogenesis of RW and provide a rationale for future exploration of the mechanistic relationship between RW and SA.
Intimate partner violence, substance use, and health comorbidities among women: A narrative review

Exposure to intimate partner violence (IPV), including physical, sexual, and psychological violence, aggression, and/or stalking, impacts overall health and can have lasting mental and physical health consequences. Substance misuse is common among individuals exposed to IPV, and IPV-exposed women (IPV-EW) are at-risk for transitioning from substance misuse to substance use disorder (SUD) and demonstrate greater SUD symptom severity; this too can have lasting mental and physical health consequences. Moreover, brain injury is highly prevalent in IPV-EW and is also associated with risk of substance misuse and SUD. Substance misuse, mental health diagnoses, and brain injury, which are highly comorbid, can increase risk of revictimization. Determining the interaction between these factors on the health outcomes and quality of life of IPV-EW remains a critical need. This narrative review uses a multidisciplinary perspective to foster further discussion and research in this area by examining how substance use patterns can cloud identification of and treatment for brain injury and IPV. We draw on past research and the knowledge of our multidisciplinary team of researchers to provide recommendations to facilitate access to resources and treatment strategies and highlight intervention strategies capable of addressing the varied and complex needs of IPV-EW.
Early post-bevacizumab change in rCBV from DSC-MRI identifies pseudoresponse in recurrent glioblastoma: Results from ACRIN 6677/RTOG 0625

Background Progressive enhancement predicted poor survival in ACRIN 6677/RTOG 0625, a multi-center trial of bevacizumab with irinotecan or temozolomide in recurrent glioblastoma, but pseudoresponse likely limited enhancement-based survival prognostication in T1 non-progressors. We aimed to determine whether early change in cerebral blood volume from baseline (ΔCBV) could further stratify the T1 non-progressors according to overall (OS) and progression-free (PFS) survival. Methods 37/123 enrolled patients had DSC-MRI, including 13, 15, and 8 patients without 2D-T1 progression at 2, 8, and 16 weeks post-treatment initiation, respectively. Mean CBV normalized to white matter (nRCBV) and mean standardized CBV (sRCBV) were extracted from enhancing tumor. ROC curves were derived for ΔCBV using six-month PFS and one-year OS as reference standards. Kaplan-Meier survival estimates and log-rank test compared PFS and OS for both ΔCBV (increase vs. decrease) and T1 response status (stable vs. decreasing enhancement). Results PFS and OS were significantly worse for increasing CBV at 2 weeks (p=0.003 and p=0.002 for nRCBV, and p=0.03 and p=0.03 for sRCBV, respectively), but not for 2D-T1 patients with stable vs. decreasing enhancement (p=0.44 and p=0.86, respectively). ΔCBV at week 2 was also a good prognostic marker for OS-1 and PFS-6 using ROC analysis. By contrast, 2D-T1 response status at weeks 2, 8, and 16 was not associated with PFS-6. ΔCBV at 16 weeks (p=0.008 for sRCBV) but not 8 weeks (p=0.74 for nRCBV and p=0.56 for sRCBV) was associated with significant difference in median survival, but no difference in survival was observed for 2D-T1 patients with stable vs. decreasing enhancement at 8 weeks (p=0.69) or 16 weeks (p=0.21). At 16 weeks, OS did not differ significantly between 2D-T1 progressors and 2D-T1 non-progressors with increasing CBV (median survival 3.3 months post week 16 scan vs. 9.2 months, respectively; p=0.13), suggesting that 2D-T1 non-progressors with increasing CBV may have a prognosis like that of 2D-T1 progressors. Conclusion After 2 weeks of anti-angiogenic therapy, ΔCBV in 2D-T1 non-progressors significantly prognosticated PFS and OS, whereas 2D-T1 response status did not, identifying a subpopulation that benefits from bevacizumab. Combining 2D-T1 progression and ΔCBV may yield a response assessment paradigm with 3-tiered OS stratification.
The occurrence of humpback whales across the Hawaiian archipelago revealed by fixed and mobile acoustic monitoring

The occurrence of humpback whales (Megaptera novaeangliae) across the 2600 km of Hawaiian archipelago, which include the remote atolls, banks, and seamounts of Papahānaumokuākea Marine National Monument (PMNM), remains poorly understood. Previous surveys for humpback whales beyond the main Hawaiian Islands have been scarce due to limited access and the challenging winter conditions typically found in PMNM when whales are present. To overcome these limitations, a combination of moored acoustic recorders and a Wave Glider autonomous surface vehicle were used to acoustically monitor eight locations and survey approximately 1500 km of the Hawaiian archipelago for the occurrence of humpback whale song during the 2019-2020 breeding season. Relative song prevalence was established using a machine learning tool and by quantifying the level of song chorusing. A generalized additive model framework was applied to understand the associations between habitat variables and humpback whale song occurrence, and sound propagation modeling was performed to examine whether acoustic propagation influenced observed patterns. Whale song was recorded at all monitored and surveyed locations across the archipelago, albeit in varying amounts. Among the locations monitored with moored recorders, the highest and most sustained seasonal chorusing levels were measured off Maui followed by French Frigate Shoals (Kānemilohai), Hawaii Island, Middle Bank, Oahu, Kauai, Gardner Pinnacles (Pūhāhonu) and Pearl and Hermes Reef (Holoikauaua), respectively. The Wave Glider mission to PMNM revealed that song prevalence was highest at Middle Bank and gradually decreased further to the northwest, reaching a minimum at Gardner Pinnacles (Pūhāhonu). However, song occurrence increased again at Raita Bank, remaining high between Raita Bank and the Northampton Seamounts. The results reveal that nearly the entire Hawaiian archipelago is exploited by humpback whales during the winter and early spring months. Moreover, song occurrence patterns suggest that there may be more structure in the distribution of whales in PMNM than previously known and raises questions about whether multiple subpopulations occur across the archipelago.
Effects of sequential inhibitory and facilitatory repetitive transcranial magnetic stimulation on neurological and functional recovery of a patient with chronic stroke: A case report and literature review

Background and purpose The effects of conventional protocols of repetitive transcranial magnetic stimulation (rTMS) in the chronic phase of stroke are limited. This study aimed to apply the sequential inhibitory and facilitatory rTMS for upper limb motor dysfunction post-stroke to observe the efficacy and explore the possible neurophysiological mechanism. We hypothesize that this protocol would both enhance the excitability of affected M1 and promote connections among motor areas. Case description We reported a 55-year-old female patient with a 1-year chronic stroke and right-sided hemiplegia, who underwent the 14-session rTMS with seven sessions of low frequency (LF) and with seven sessions of high frequency (HF). Clinical scales mainly including Fugl-Meyer Assessment of Upper Extremity (FMA-UE), Action Research Arm Test (ARAT), neurophysiological measures, and functional near-infrared spectroscopy (fNIRS) were assessed before (T0), at the midpoint (T1), and after the intervention (T2). Outcomes The patient exhibited post-intervention improvement in upper extremity function. There was increased excitability in the ipsilesional hemisphere and the opposite in the contralesional hemisphere. The interhemispheric inhibition (IHI) ratio increased from 2.70 to 10.81 and finally decreased to 1.34. Oxy-Hb signal was significantly decreased in affected M1 and mildly decreased in unaffected M1, while that of PMC and SMA on the affected side increased significantly. Conclusion The sequential inhibitory and facilitatory rTMS significantly promoted motor recovery in the patient. Related mechanisms include upregulation of excitability in the ipsilesional hemisphere, return of interhemispheric balance, and neuroplasticity-induced cortical reorganization.
Weighted gene co-expression network analysis identifies genes related to HG Type 0 resistance and verification of hub gene GmHg1

Introduction The soybean cyst nematode (SCN) is a major disease in soybean production thatseriously affects soybean yield. At present, there are no studies on weighted geneco-expression network analysis (WGCNA) related to SCN resistance. Methods Here, transcriptome data from 36 soybean roots under SCN HG Type 0 (race 3) stresswere used in WGCNA to identify significant modules. Results and Discussion A total of 10,000 differentially expressed genes and 21 modules were identified, of which the module most related to SCN was turquoise. In addition, the hub gene GmHg1 with high connectivity was selected, and its function was verified. GmHg1 encodes serine/threonine protein kinase (PK), and the expression of GmHg1 in SCN-resistant cultivars (‘Dongnong L-204’) and SCN-susceptible cultivars (‘Heinong 37’) increased significantly after HG Type 0 stress. Soybean plants transformed with GmHg1-OX had significantly increased SCN resistance. In contrast, the GmHg1-RNAi transgenic soybean plants significantly reduced SCN resistance. In transgenic materials, the expression patterns of 11 genes with the same expression trend as the GmHg1 gene in the ‘turquoise module’ were analyzed. Analysis showed that 11genes were co-expressed with GmHg1, which may be involved in the process of soybean resistance to SCN. Our work provides a new direction for studying the Molecular mechanism of soybean resistance to SCN.