Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and immune landscape evolution defines subtypes of MMR deficient colorectal cancer

Mismatch repair deficient colorectal cancers have high mutation loads and many respond to immune checkpoint-inhibitors. We investigated how genetic and immune landscapes co-evolve in these tumors. All cases had high truncal mutation loads. Driver aberrations showed a clear hierarchy despite pervasive intratumor heterogeneity: Those in WNT/βCatenin, mitogen-activated protein kinase and TGFβ receptor family genes were almost always truncal. Immune evasion drivers were predominantly subclonal and showed parallel evolution. Pan-tumor evolution, subclonal evolution, and evolutionary stasis of genetic immune evasion drivers defined three MMRd CRC subtypes with distinct T-cell infiltrates. These immune evasion drivers have been implicated in checkpoint-inhibitor resistance. Clonality and subtype assessments are hence critical for predictive immunotherapy biomarker development. Cancer cell PD-L1 expression was conditional on loss of the intestinal homeobox transcription factor CDX2. This explains infrequent PD-L1 expression by cancer cells and likely contributes to the high recurrence risk of MMRd CRCs with impaired CDX2 expression.
Anatomical characteristics for identification and quality indices of four promising commercial bamboo species in Java, Indonesia

The anatomical characteristics in the culms of the four promising Indonesian bamboo species, including Dendrocalamus asper, Dendrocalamus giganteus, Bambusa vulgaris var. vulgaris, and Bambusa vulgaris var. striata, were investigated to produce an identification key and quality indices for further effective utilization. The crystalline properties of the bamboo culm were determined using X-ray diffraction analysis. Dendrocalamus asper and Bambusa vulgaris var. striata showed vascular bundle type IV, while Dendrocalamus giganteus and Bambusa vulgaris var. vulgaris displayed vascular bundle type III. The vascular bundle density in the bamboo culms increased from the bottom to the top part and was higher in the outer part than in the inner part. The fiber portion and length in the outer part were higher than those in the inner part, opposite of those in the parenchyma portion. Dendrocalamus giganteus had the largest vessel and parenchyma diameter, while Bambusa vulgaris var. vulgaris had the smallest. Bambusa vulgaris var. vulgaris had the longest parenchyma, while Bambusa vulgaris var. striata and Dendrocalamus giganteus had the shortest. The outer part of the four bamboo culms showed higher relative crystallinity than the inner part. All anatomical parameters, except for crystallite width, showed a variation in the radial direction of the four bamboo culms but did not show a consistent tendency vertically. This study revealed that the anatomical properties were different between bamboo species and could be used for species identification and quality evaluation indices of the culms.
Effect of High Power Laser Therapy on Patients with Chronic Discogenic Sciatica: A Randomized Clinical Trial

Back Ground: Sciatica is a frequent clinical illness that may be intensely painful, disabling, and life-altering. Objectives: The goal of this research was to see how high-power laser therapy affects the intensity of pain, angle of straight leg raise, six-minute walk test and electrophysiological studies in patients with chronic discogenic sciatica. Methods: A lumbar disc herniation at L5-S1 caused chronic unilateral sciatica in thirty-six male patients were included in this study. The patients have been divided into 2 identical groups [the control group (G1) and the study group (G2)] randomly. Participants in the control group (G1) got a designed physiotherapy program that included ultrasound, stretching exercise, back muscles strengthening exercise and sciatic nerve flossing technique. While patients in the study group (G2) got the same designed physiotherapy program as G1 plus high power laser therapy (HPLT). The outcome measures were latency and amplitude of Hoffmann reflex (H-reflex) for evaluating S1 nerve root function, visual analog scale (VAS) for evaluating pain level, angle of straight leg raise (SLR) and six-minute walk test (6MWT) for assessing functional impairment. Both groups were assessed before and after 4 weeks of therapy. Results: The findings demonstrated that both groups showed a significant reduction in pain level and latency of H-reflex following therapy. The angle of SLR, 6-minute walking distance (6MWD), and the amplitude of the H-reflex all improved significantly in both groups. After therapy, the study group's VAS and H reflex latency were significantly decreased than the control group's (p < 0.01). In addition, the study group's 6MWD, angle of SLR, and H reflex amplitudes were significantly increased than the control group's (p < 0.01) following therapy. Conclusion: High power laser therapy (HPLT) is a successful treatment for patients suffering from chronic discogenic sciatica.
Oral and Intestinal Bacterial Substances Associated with Disease Activities in Patients with Rheumatoid Arthritis: A Cross-Sectional Clinical Study

Intestinal bacterial compositions of rheumatoid arthritis (RA) patients have been reported to be different from those of healthy people. Dysbiosis, imbalance of the microbiota, is widely known to cause gut barrier damage, resulting in an influx of bacteria and their substances into host bloodstreams in animal studies. However, few studies have investigated the effect of bacterial substances on the pathophysiology of RA. In this study, eighty-seven active RA patients who had inadequate responses to conventional synthetic disease-modifying antirheumatic drugs or severe comorbidities were analyzed for correlations between many factors such as disease activities, disease biomarkers, intestinal bacterial counts, fecal and serum lipopolysaccharide (LPS), LPS-binding protein (LBP), endotoxin neutralizing capacity (ENC), and serum antibacterial substance IgG and IgA antibody levels by multiple regression analysis with consideration for demographic factors such as age, sex, smoking, and methotrexate treatment. Serum LBP levels, fecal LPS levels, total bacteria counts, serum anti-LPS from Porphyromonas gingivalis (Pg-LPS) IgG antibody levels, and serum anti-Pg-LPS IgA antibody levels were selected for multiple regression analysis using Spearman's correlation analysis. Serum LBP levels were correlated with disease biomarker levels, such as erythrocyte sedimentation rate (p < 0.001), C-reactive protein (p < 0.001), matrix metalloproteinase-3 (p < 0.001), and IL-6 (p = 0.001), and were inversely correlated with hemoglobin (p = 0.005). Anti-Pg-LPS IgG antibody levels were inversely correlated with activity indices such as patient global assessments using visual analogue scale (VAS) (p = 0.002) and painVAS (p < 0.001). Total bacteria counts were correlated with ENC (p < 0.001), and inversely correlated with serum LPS (p < 0.001) and anti-Pg-LPS IgA antibody levels (p < 0.001). These results suggest that substances from oral and gut microbiota may influence disease activity in RA patients.
Long-range Dependencies of Euronext Capital Markets: A Dynamic Detrended Analysis

This paper aims to test efficiency, in its weak form, in the cap­ital markets of the Netherlands (AEX), Belgium (BEL 20), France (CAC 40), Ireland (ISEQ 20), Norway (OSEBX), Portugal (PSI 20), in the period from April 4, 2019 to April 1, 2021. The sample was partitioned into two sub­periods, the first and second wave of the global pandemic: April 4, 2019 to April 30, 2020; May 4, 2020 to April 1, 2021. To carry out this analysis, different approaches were undertaken to analyze whether: (i) Euron­ext’s stock markets have more significant long memories in the first or second wave of the global pandemic? The results show the presence of sharp long memories during the first wave of the global pandemic, par­ticularly in the stock indices OSEBX (0.67), PSI 20 (0.67), AEX (0.66), BEL 20 (0.64), CAC 40 (0.62), ISEQ 20 (0.61), which implies that the yields are au­tocorrelated in time and, there is a reversal of the average, in all indexes. Regarding the second wave of the global pandemic, we found that most Euronext stock markets don’t reject the random walk hypothesis, with the exception of the Norwegian (0.56) and Portugal (0.55) stock markets. These findings show that the impact of the Covid-19 pandemic was ac­centuated during the first wave, but from May 2020 the markets adjust­ed and showed balance. The authors believe that the results achieved will be a benefit to international investors seeking efficient diversifica­tion into their portfolios.
A hybrid speed choice model: the role of human factors

ABSTRACT Using a roadside survey among 1026 drivers and recording actual mean speed of vehicles, we develop a hybrid speed choice model to investigate the simultaneous effects of latent psychological and manifest variables in speed choice analysis. The latent variable part measures psychological factors derived from the theory of planned behavior (TPB). The results show that most factors of the TPB including attitudes, perceived behavioral control and intentions significantly predicted speed choice behavior. Females and older drivers (>60 years) have stronger attitudes and intentions to comply with the speed limit, which in turn, are positively related to slow driving behavior (<100 km/h) in freeways. Policy-scenario analyses show that an enhancement (one-point increase in the Likert scale) in attitudes and intentions to comply with the speed limit range would decrease the share of fast driving (>120 km/h) by around 5.5% (from 15% to 9.5%) and 3.5% (from 15% to 11.5%), respectively.
Anxiety and Depression among Family Caregivers of Children with Epilepsy in Burkina Faso

Background Epilepsy is a common and chronic neurological disorder influencing children's cognitive and behavioral performance. Primary caregivers of children with epilepsy (CWE) report high levels of depression and anxiety. Patients and Methods We performed a cross-sectional study on caregivers of CWE in the Neurology Department of Yalgado Ouédraogo University Teaching Hospital from May 7, 2020 to August 18, 2020. The State-Trait Anxiety Inventory scale and Beck Depression Inventory scale were assessed to screen anxiety and depression. Results One hundred caregivers with a mean age of 37.75 ± 10.69 years were included in the study. The majority of them were female gender (73%), aged <40 years (59%), and residing in rural areas (79%). Most of caregivers were female gender (73%) and the mothers of children (67%). The majority of CWE were boys (55%), having generalized epilepsy (55%) and epilepsy duration less than 6 years (74%). Anxiety was observed in 56%, depression in 27%, and both anxiety and depression in 23% of caregivers. The factors influencing anxiety among caregivers were female gender (p = 0.04), being patient's mothers (p = 0.04), and caring male patients (p = 0.04). The factors associated with caregiver's depression were being married (p = 0.03) and caring patients with five seizures per year (p = 0.04). Conclusion The study revealed very high rates of anxiety and depressive disorder among caregivers of CWE in Burkina Faso.
The orientation of Australian coursework-focussed marketing masters degree

Using content analysis, this paper examines the orientation of Australian coursework masters degrees in marketing by analysing data collected from 38 university websites on the entry requirements, degree structure and research opportunities of the programs. The findings indicate that there appears to be an attempt to offer programs aiming at a range of “outcomes”, i.e. training for PhD, advanced studies in marketing, or accreditation for those in the industry. The diverse orientation of the degrees offered means that Australian institutions are potentially facing a challenge, targeting programs at different market segments.
The Relationship Between Vitamin D Status and the Clinical Severity of COVID-19 Infection: A Retrospective Single-Center Analysis

Background and objective Some studies have suggested a potential protective role of vitamin D in coronavirus disease 2019 (COVID-19) patients, and this has led to a debate on the topic in the medical community. However, the reported data on the number of hospitalized patients who were vitamin D-deficient is not convincing. In light of this, the aim of the present study was to explore if vitamin D deficiency is correlated with severity and mortality rates of COVID-19 infection in hospitalized COVID-19 patients at a tertiary care hospital in Greece. Methods We conducted a single-center retrospective study involving 71 patients hospitalized with COVID-19 from August to October 2020. Serum 25-hydroxyvitamin D (25(OH)D) level was assessed in all patients within 48 hours of hospital admission. Serum 25(OH)D level ≤20 ng/ml was defined as a deficiency, while that >20 ng/ml as repletion. The primary outcomes of the infection were classified as partial/complete recovery and mortality during hospitalization. The secondary outcomes were blood markers of inflammation and thrombosis. Results Among the 71 COVID-19-positive patients [mean age: 63 years, range: 20-97; male (n=47; 66.2%): female (n=24; 33.8%)] who were enrolled in the study, 46 (64.8%) patients had 25(OH)D levels ≤20 ng/ml and 25 (35.2%) had a level >20 ng/ml. According to the patients' medical history, 55 patients (77.5%) had comorbidities. It appears that vitamin D deficiency (<20 ng/ml) significantly correlated with elevated biochemical markers such as procalcitonin and troponin (p<0.001). Moreover, male gender, advanced age (>60 years), and comorbidities were positively associated with more severe COVID-19 infection (elevated inflammation markers, radiographic findings on X-rays, and increased length of hospital stay). Conclusion These preliminary findings show that vitamin D status among the patients was not related to the severity of COVID-19 infection.
The development of a hybrid model to forecast paddy water temperature as an alert system for high‐temperature damage

Climate change has led to increasing global air temperatures. In the field of crop cultivation, long‐term high temperatures (heatwaves) during the rice‐growing season might increase the risk of high‐temperature damage to rice, which might result in reductions to the yield and quality of rice. In this study, a hybrid forecast model consisting of a combined paddy field heat balance model and a meteorological forecast model is proposed for predicting 1‐day‐ahead water temperatures as an alert system for high‐temperature damage to paddy fields, with resolution in terms of hours. The results show close agreement between the measured and predicted water temperatures, and the high‐temperature alert accuracy was 88.5%. Additionally, the climate resilience of paddy fields was investigated by using the rising annual temperatures due to climate change. The observations indicate that while paddy fields are sensitive to the climate, their climate resilience can be improved through artificial measures. Farmers and managers of paddy fields can thus be made aware of the water temperatures of the paddy fields in advance to enable reasonable management of water resources and avoid high‐temperature damages caused by extreme weather conditions.
Intravitreal Trans-Resveratrol Ameliorates NMDA-Induced Optic Nerve and Retinal Injury

Abstract Purpose Retinal and optic nerve damage in glaucoma involves excitotoxicity via N-methyl-D-aspartate (NMDA) receptors. Since, trans-resveratrol (TR) is known to provide neuroprotection, we investigated its protective effects against NMDA-induced retinal and optic nerve injury. Methods Sprague Dawley rats were divided into four groups which received vehicle (PBS), NMDA, and TR 0.4 or TR 4 nmol 24 h prior to NMDA, unilaterally and intravitreally. Seven days post-injection, rats were euthanized; eyeballs were enucleated and subjected to hematoxylin and eosin and terminal transferase dUTP nick end labeling staining while optic nerves were isolated for toluidine blue staining. Results Retinal morphometry showed that ganglion cell layer (GCL) layer thickness within inner retina (IR), retinal cell count (RCC) per 100-µm length of GCL, RCC per 100-µm2 area of GCL, and RCC per 100 µm2 of IR were significantly higher in both TR-treated groups compared to the NMDA group. No differences were observed between the two dose groups. Optic nerve morphology was in accordance with the retinal morphology whereby TR-treated groups showed significantly lesser degenerative changes compared to NMDA-treated group. Conclusions TR protects against NMDA-induced changes in retinal and optic nerve morphology by preventing retinal cell apoptosis.
cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions

Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants unanalyzed. In this work, we introduce cumulative LD (cLD), a stable statistic that captures the rare-variant LD between genetic regions, which reflects more biological interactions between variants, in addition to lack of recombination. We derived the theoretical variance of cLD using delta methods to demonstrate its higher stability than LD for rare variants. This property is also verified by bootstrapped simulations using real data. In application, we find cLD reveals an increased genetic association between genes in 3D chromatin interactions, a phenomenon recently reported negatively by calculating standard LD between common variants. Additionally, we show that cLD is higher between gene pairs reported in interaction databases, identifies unreported protein-protein interactions, and reveals interacting genes distinguishing case/control samples in association studies.
Differences in running velocity and boldness between male and female Atlantic sand fiddler crab (Leptuca pugilator)

Atlantic sand fiddler crabs (Leptuca pugilator) exhibit an extreme case of sexual dimorphism with the male crabs wielding an enlarged dominate claw that can account up to 40% of an individual’s total body mass. The salt pans found in marine marshes are commonly colonized by fiddler crabs and have limited coverage from avian predators, making the ability to quickly run back their burrows, an important part of life. After threats have passed, making the decision of when to exit is important for securing resources and finding a mate, but if done too early could mean falling victim to a predator. This study pairs experiments and observations to determine if crab anatomy or personality is more important influence on running velocity and boldness. Crabs (21 males & 21 females) were ran and timed on a sand racetrack for 1m, behavior assays were conducted to determine each individuals boldness, and measurements of various anatomical measurements were taken. Female crabs were found to have faster run velocities than male crabs. However, male crabs displayed bolder behavior than female crabs. Overall, personality was found to be the most important factor on a crab’s running velocity and boldness.
Uncovering a new form of digitally-enabled agility: an improvisational perspective

ABSTRACT Agile organisations address changes with ease and speed. These changes are tackled through the concept of ongoing agility, using a sense-respond process, composed of sensing, decision-making, and acting. Increasingly, however, unexpected events require a different agility response. In this study, we propose and empirically examine how improvisational agility – conceptualised as organisation improvisational capability, the ability to sense and respond to unexpected events with speed and creativity – is a type of agility better suited for unanticipated events. Specifically, we focus on the improvisational agility sense-respond process. Using four exploratory cases, we find that organisations can leverage existing ongoing agility mechanisms for improvisational agility and, through learning, can leverage improvisational agility in ongoing agility. We also explain how different components of information management capability support improvisational agility, depending on the unexpected events and the need for speed or creativity.
A personalized Reflection on Online Education in Morocco: Pedagogical Gains and Pittfalls

This paper aspires to provide a reflection, inspired from personal experience, on online education at the university level in Morocco. The data has been gathered by means of recently published literature on online education to enable the researcher to be at a better position to critically evaluate concepts, methodologies and teaching approaches in tandem with online education. The use of information technology to publicly promote the renewal and revival of education in general and teaching in particular is a blatant epistemological marker of our education model’s progress in terms of digitalization and computerization of educational resources via different robust national programs, such as MARWAN (2002), GENIE (2005), NAFIDA (2008), INJAZ (2009) and LAWHATI (2015). In fact, this has given rise to emerging technologies, such as Artificial Intelligence (AI), Big Data (BD) and the Internet of Things (IOT). In this regard, it must be noted that the current Moroccan education system exhibits diversified online education trends both in form and content, and thus this new paradigm of learning abundantly introduces various types of intelligent education systems and platforms that emerge on a perpetual basis. Owing to this conscious online shift, both the class content and the learning context of students can be tracked and monitored at any time, which is directly conducive to fathoming out the individualization and differentiation of students in a timely manner.
S0031182021001542jra 51..58

Mammalian haemosporidian parasites are classified in ten genera, including Plasmodium, Hepatocystis and Nycteria. A high diversity of haemosporidian parasites has been described from bats, but our understanding of their prevalence, distribution and use of hosts remain fragmented. The haemosporidian parasites of bats in Cameroon have been largely understudied, but here, bats, sampled from different habitat types of the Central Region of Cameroon, were investigated for haemosporidian infections with a combination of microscopic and molecular phylogenetic analysis. An overall prevalence of 18.1% of haemosporidian infections was detected in a total of 155 investigated bats belonging to 14 bat species. For the first time Hepatocystis and Nycteria parasites were detected in bats from Cameroon and molecularly characterized. Hepatocystis infections were exclusively identified in the epauletted fruit bat host species Epomophorus pusillus with a high prevalence of 65.5%, whereas Nycteria infections could be detected in several hosts, namely: Doryrhina cyclops (60.0%), Rhinolophus landeri (20.0%) and one Nycteris grandis. This study unveils evidence that habitat types may play a role in transmission of Hepatocystis parasites on a local scale and it adds important information on the distribution and host specificity of the neglected haemosporidian genus Nycteria.