Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and Phylogenetic Analysis of Viruses Linked with Fig Mosaic Disease in Seventeen Fig Cultivars in Palestine

Fig mosaic is a viral disease (FMD) that spreads in Palestinian common fig ( Ficus carica L.) orchards. Recognizing the economic value of fig plants and the harmful nature of FMD, the disease poses a significant threat to the economy of the fig production in Palestine. We applied the reverse transcription and amplification (RT-PCR) and PCR technique to leaf samples of 77 trees and 14 seedlings of 17 fig cultivars. The samples were collected from orchards in the main fig-growing provinces of the Palestinian West Bank, to assess the prevalence of viruses associated with FMD, and confirm a possible link of symptoms with viruses detected. Four viruses were detected: Fig mosaic virus (FMV), Fig badnavirus-1 (FBV-1), Fig leaf mottle-associated virus 2 (FLMaV-2), and Fig fleck-associated virus (FFkaV). FMV and FBV-1 were found in all tested fig plants (100%), while FLMaV-2 and FFkaV were detected in 61.5% and 33% of the fig samples, respectively. The high incidence of FBV-1 in the newly propagated symptomatic and symptomless seedlings from different cultivars may be an indication that FBV-1 is integrated into the genome of the fig in a cultivar nondiscriminatory manner. Very weak or no association was detected between FMD symptoms severity in the 17 Palestinian fig cultivars with the various viruses’ combinations observed (i.e., number of the viruses infecting the plant). These results support the notion that FMD symptom severity expression is likely to be controlled by a combination of FMV infection, cultivars, and environmental factors, rather than the number of viruses infecting the plant.
Primary thymic mucosa-associated lymphoid tissue lymphoma complicated with renal amyloidosis

Abstract Introduction: Primary mucosa-associated lymphoid tissue (MALT) lymphomas originating in thymus is rare. And, there have been few reports of patients with MALT coexisting with amyloidosis. As far as we know, this was the first case report on MALT lymphoma associated with renal amyloidosis. Patient concerns: A 57-year-old man presented with nephrotic syndrome. Further workup revealed IgM-Lambda type monoclonal gammopathy. Bone marrow biopsy showed 8% clonal plasma cells. Renal biopsy confirmed the diagnosis of Lambda light chain AL amyloidosis. positron emission tomography/computed tomography showed thymic lesions which upon biopsy were diagnosed as MALT lymphoma of the thymus. Diagnosis: Primary thymic MALT lymphoma complicated with renal amyloidosis. Interventions: The patient underwent surgical resection of the thymus mass and 2 courses of chemotherapy. Outcomes: Follow-up data showed that the patient survived 18 months after surgical excision and chemotherapy. Conclusion: The case highlights the importance of screening for malignancy in patients with renal amyloidosis.
Unilateral percutaneous kyphoplasty for lumbar spine

Abstract Anatomical differences of unilateral percutaneous kyphoplasty (PKP) between transverse process-pedicle approach (TPPA) and conventional transpedicular approach (CTPA) are not well discussed. To investigate the anatomical distinctions of unilateral PKP between TPPA and CTPA, we have discussed the unilateral PKP through a 3-dimensional-computed tomography database. Five hundred lumbar spines from 100 patients have been retrospectively collected and unilateral CTPA and TPPA were simulated. Distance between the entry point and the midline of the vertebral body (DEM), the puncture inclination angle (PIA), and the success rate (SR) of puncture were measured and compared. The male presented with significantly larger DEM than the female. The TPPA group presented with larger DEM than the CTPA group according to different level, the difference was 1.5 ± 1.1 mm to 3.8 ± 2.3 mm. The PIAs in the TPPA group were larger than that in the CTPA group. The SR including 1 side SR and bilateral SR was 72.0% in the CTPA group and 98.0% in the TPPA group. Compared with CTPA group, the SR in TPPA group was significantly higher for L1 to L4 no matter in the left, right side and female patients. The TPPA group presented with more lateral entry point, larger PIAs and higher SRs than that in the CTPA group. PKP surgery through a TPPA was safer and could provide a more symmetrical distribution of bone cement than the CTPA group.
A model for COVID-19 transmission in Connecticut

To support public health policymakers in Connecticut as they begin phased lifting of social distancing restrictions, we developed a county-structured compartmental SEIR-type model of SARS-CoV-2 transmission and COVID-19 disease progression. We calibrated this model to the local dynamics of deaths and hospitalizations and the exact timing of state interventions, including school closures and stay-at-home order. In this technical report, we describe the details of the model design, implementation and calibration, and show projections of epidemic development through the Summer of 2020 under different assumptions about the increase in contact rates following partial state reopening. Our model results are consistent with high effectiveness of state lockdown measures, but changes in human interaction patterns during the coming months are unknown. In addition, a lot of uncertainty remains with respect to several key epidemiological parameters and the effectiveness of increased testing and contact tracing capacity. As more information becomes available, we will update the projections presented in this report. Reports in this series are posted to https://crawford-lab.github. io/covid19_ct/.
Risk and Severity of COVID-19 and ABO Blood Group in Transcatheter Aortic Valve Patients

Background: Although cardiovascular disease has been associated with an increased risk of coronavirus disease 2019 (COVID-19), no studies have reported its clinical course in patients with aortic stenosis who had undergone transcatheter aortic valve replacement (TAVR). Several observational studies have found an association between the A blood group and an increased susceptibility to SARS-CoV-2 infection, whereas the O blood group appears to be protective. Objective: To investigate the frequency and clinical course of COVID-19 in a large sample of patients who had undergone TAVR and to determine the associations of the ABO blood group with disease occurrence and outcomes. Methods: Patients who had undergone TAVR between 2010 and 2019 were included in this study and followed-up through the recent COVID-19 outbreak. The main outcomes were the occurrence and severity (hospitalization and/or death) of COVID-19 and their association with the ABO blood group. Results: Of the 1125 patients who had undergone TAVR, 403 (36%) died before January 1, 2020, and 20 (1.8%) were lost to follow-up. The study sample therefore consisted of 702 patients. Among them, we identified 22 cases (3.1%) with COVID-19. Fourteen patients (63.6%) were hospitalized or died of disease. Multivariate analysis identified the A blood group (versus others) as the only independent predictor of COVID-19 in patients who had undergone TAVR (odds ratio [OR] = 6.32; 95% confidence interval [CI] = 2.11-18.92; p=0.001). The A blood group (versus others; OR = 8.27; 95% CI = 1.83-37.43, p=0.006) and a history of cancer (OR = 4.99; 95% CI = 1.64-15.27, p = 0.005) were significantly and independently associated with disease severity (hospitalization and/or death). Conclusions: Patients who had undergone TAVR are vulnerable to COVID-19. The subgroup with the A blood group was especially prone to develop the disease and showed unfavorable outcomes.
Risk of death by age and gender from CoVID-19 in Peru, March-May, 2020

Peru implemented strict social distancing measures during the early phase of the epidemic and is now experiencing one of the largest CoVID-19 epidemics in Latin America. Estimates of disease severity are an essential indicator to inform policy decisions about the intensity and duration of interventions needed to mitigate the outbreak. Here we derive delay-adjusted case fatality rates (aCFR) of CoVID-19 in a middle-income country in South America. We used government-reported time series of CoVID-19 cases and deaths stratified by age group and gender. Our estimates as of May 25, 2020, of the aCFR for men and women are 10.8% (95%CrI: 10.5-11.1%) and 6.5% (95%CrI: 6.2-6.8%), respectively, and an overall aCFR of 9.1% (95%CrI: 8.9-9.3%). Our results show that senior individuals are the most severely affected by CoVID-19, particularly men, with aCFR of almost 60% for those aged 80- years. We found that men have a significantly higher cumulative morbidity ratio than women across most age groups (proportion test, p-value< 0.001), with the exception of those aged 0-9 years. The COVID-19 epidemic is imposing a large mortality burden in Peru. Senior individuals, especially those who are older than 70 years of age, are being disproportionately affected by the COVID-19 pandemic.
Influence of Eimeria spp. Infection on Chicken Jejunal Microbiota and the Efficacy of Two Alternative Products Against the Infection

SUMMARY. Eimeria spp. are important intestinal pathogens of chickens (Gallus gallus domesticus). Anticoccidial feed additives, chemicals, and ionophores have traditionally been used to control Eimeria infections in broiler production. Thus, the trend toward antibiotic-free and organic production requires new approaches to coccidiosis prevention. Two not mutually exclusive methods are the use of plant extracts with antiparasitic activity and manipulation of the intestinal microbiota by pre- and probiotics. In the present study, birds were inoculated with a combination of Eimeria acervulina, Eimeria maxima, and Eimeria tenella. We profiled the jejunal microbiome at multiple time points postinfection to investigate the changes in jejunum microbiota and to identify the time point of the maximum difference between infected and noninfected birds. Additionally, we assessed the anticoccidial effects of two anecdotal treatment methods, green tea and apple cider vinegar, as well as amprolium. Green tea and apple cider vinegar had no effect on oocyst shedding, but green tea reduced the mild unspecific lesions in coccidia-infected birds; there was no influence on unspecific lesions in uninfected controls. Jejunal contents were collected on the day of the infection and 1, 2, 4, 6, 10, and 14 days postinfection (dpi) for investigation of the intestinal microbiota by 16S ribosomal (r)RNA gene sequencing. Comparison of the untreated-uninfected and the untreated-infected groups showed a maximum community dissimilarity of 10 dpi. From 4 days after infection, Clostridiales were significantly enriched at the expense of Lactobacillales in infected compared with uninfected birds. Interestingly, treatment with green tea prevented proliferation of Clostridiales induced by the coccidia and increased the relative abundance of Melainabacteria.
High Prevalence of Avian Influenza Virus Among Wild Waterbirds and Land Birds of Mexico

SUMMARY. Aquatic wild birds, especially waterfowl, have been long considered the main reservoirs of the avian influenza A virus; however, recent surveys have found an important prevalence of these viruses among land birds as well. Migration has been suggested as an important factor in the avian influenza virus dissemination. We aimed to estimate the prevalence of influenza A viruses in wild birds (waterbirds and land birds; resident and migratory) in eastern Mexico, where the three main North American migration flyways converge and where there was no previous information on this subject. We detected influenza with reverse transcription coupled with a PCR approach. Of the 534 birds sampled between 2010 and 2012, we detected the influenza A virus in a high proportion of birds (39%). Prevalence was particularly high in land birds (49%) when compared to aquatic birds (26%); there was no difference in overall prevalence between resident (39%) and migratory birds (39%). The high prevalence of the avian influenza virus in land birds was noteworthy in the innermost sampling areas in northern Mexico (Coahuila [82%] and Nuevo Leon [43%]).
Chapter 6 The Loyalty Islands and Ridge, New Caledonia

Abstract The Loyalty Ridge lies to the east and NE of the Norfolk Ridge. The three main Loyalty Islands (Maré, Lifou and Ouvéa) emerge from the ridge at the same latitude as Grande Terre. The islands are uniformly composed of carbonate deposits, except for Maré, where Middle Miocene intra-plate basalts and associated volcaniclastic rocks form restricted outcrops. Miocene rhodolith limestones constitute the bulk of the carbonate cover of the three islands. On Maré, these platform accumulations are locally topped by a dolomitic hardground, which, in turn, is covered by Pliocene–Pleistocene coral-bearing formations. These coral reef constructions are preserved as elevated rims over all three islands and define an atoll stage in their development. The Pleistocene–Holocene palaeoshoreline indicators include fringing bioconstructions and marine notches and record both eustatic sea-level changes and tectonic deformation. The ridge has been in the forebulge region in front of the active Vanuatu subduction zone since the Pliocene and each of the three islands has been uplifted and tilted to varying degrees. Offshore, the Loyalty Ridge continues northwards to the d'Entrecasteaux Zone and southwards to the Three Kings Ridge. Although typically volcanic, the nature of the deep Loyalty Ridge remains unknown.
Chapter 7 Post-obduction evolution of New Caledonia

Abstract The post-obduction formations of Grande Terre, New Caledonia, comprise igneous intrusions, regolith cover, and marine and terrestrial sedimentary rocks. Two restricted Late Oligocene granitoid bodies are intruded into the Peridotite Nappe and its substrate in the south of the island. Thick regolith cover developed over the Peridotite Nappe from the Late Oligocene or earlier. The Népoui Group comprises Late Oligocene–Early Miocene mixed marine carbonate and siliciclastic deposits. It mainly reworks the Peridotite Nappe and its regolith cover. Its development pattern is mainly controlled by tectonic uplift and subsidence. The Gwa N'Doro Formation on the eastern coast and the Fluvio-lacustrine Formation in the south are remnants of the Miocene–Present river network. Offshore, thick Oligocene to Neogene sedimentary successions are imaged by seismic surveys on the margins of Grande Terre, although these successions have not been drilled and remain undated. Several dredges have recovered shallow Miocene sedimentary rocks, indicating substantial Neogene subsidence. Quaternary formations are represented inland by aeolianite, vertisols and calcrete and offshore by the large barrier reef–lagoon complex, the onset of which is dated at c. 400 ka. This chapter discusses the different models proposed for the post-obduction evolution of Grand Terre.
Therapist vibe: children's expressions of their emotions through storytelling with a chatbot

Storytelling can develop children's emotional intelligence when they are asked to freely talk about their emotions. While parents are responsible for teaching emotional intelligence, studies in using affective technologies to help people become aware of their emotions have also been explored. In this paper, we investigate the opportunity of this technology in enabling children to recognize and express their emotions. We describe a chatbot that leverages storytelling strategies to listen to children as they share emotional events they experienced, then guides them through reflective discipline to devise the next course of action. We report the types of emotions children choose to share with the chatbot, the kinds of support that the chatbot provided, the challenges during the conversation and children's perception of the chatbot. From our findings, we suggest design considerations for a conversation flow that anchors on storytelling to support child-agent interaction.
Learning to Recognize Handwriting Input with Acoustic Features

For mobile or wearable devices with a small touchscreen, handwriting input (instead of typing on the touchscreen) is highly desirable for efficient human-computer interaction. Previous passive acoustic-based handwriting solutions mainly focus on print-style capital input, which is inconsistent with people's daily habits and thus causes inconvenience. In this paper, we propose WritingRecorder, a novel universal text entry system that enables free-style lowercase handwriting recognition. WritingRecorder leverages the built-in microphone of the smartphones to record the handwritten sound, and then designs an adaptive segmentation method to detect letter fragments in real-time from the recorded sound. Then we design a neural network named Inception-LSTM to extract the hidden and unique acoustic pattern associated with the writing trajectory of each letter and thus classify each letter. Moreover, we adopt a word selection method based on language model, so as to recognize legislate words from all possible letter combinations. We implement WritingRecorder as an APP on mobile phones and conduct the extensive experimental evaluation. The results demonstrate that WritingRecorder works in real-time and can achieve 93.2% accuracy even for new users without collecting and training on their handwriting samples, under a series of practical scenarios.
Pengunaut trainer: a playful VR app to prepare children for MRI examinations: in-depth game design analysis

We present the concept, design, and evaluation of a playful mobile virtual reality (VR) app for children to reduce anxiety and stress during MRI examinations. The Pengunaut Trainer aims to help children to familiarize themselves with the medical environment so that they can be examined without fear, rendering sedation unnecessary. The young patients learn about the procedure and train to lie still during a virtual MRI scan. We conducted a clinical trial focusing on an in-depth analysis of the game design. 29 children trained over 14 days on average before their MRI examination. The participants were impressed by the VR experience and motivated to train. They reported high levels of immersion and positive affect. Anxiety and negative feelings towards the upcoming MRI examination were significantly reduced after the training period. Moreover, our results indicate that the Pengunaut Trainer could be effective in reducing anxiety and stress during the MRI scan. Our results and the positive feedback from parents and medical professionals prove the validity of our approach.
Safety and Efficacy of Tirofiban in Rescue Treatment for Acute Intracranial Intraprocedural Stent Thrombosis

Background and Purpose: The incidence of acute intraprocedural stent thrombosis (AIST) during stenting of intracranial atherosclerotic stenosis (ICAS) has seldom been reported and evidence regarding the treatment of AIST is lacking. We aim to investigate the incidence of AIST during stenting of ICAS in our institute, assess the preliminary efficacy and safety of rescue treatment of tirofiban for these patients. Methods: From September 2016 to May 2019, all symptomatic ICAS patients who underwent intracranial stenting in our institute were prospectively registered into this study, of which patients with AIST were retrospectively reviewed to extract baseline characteristics, perioperative management, procedural details, angiographic, and clinical outcomes. Rescue treatment of tirofiban for AIST was assessed by recanalization of the culprit vessel and periprocedural death, hemorrhage, and ischemic stroke. Results: Acute intraprocedural stent thrombosis developed in 12 (6.2%) patients within 30 min after stent placement of 194 patients. All 12 cases were successfully recanalized with modified Treatment in Cerebral Ischemia (mTICI) 3 and Arterial Occlusive Lesion (AOL) 3 after rescue treatment of tirofiban alone. There was no perioperative death or any hemorrhagic complication. Three patients suffered perioperative ischemic stroke. Conclusions: We observed a non-negligible rate of AIST during intracranial stenting procedures for ICAS. Intra-arterial bolus followed by intravenous tirofiban infusion seems to be efficacious and safe for AIST during stent placement for ICAS, without increasing the rate of hemorrhagic complications and death.
Transcriptional Profiles of Skeletal Muscle Associated With Increasing Severity of White Striping in Commercial Broilers

Development of the white striping (WS) abnormality adversely impacts overall quality of broiler breast meat. Its etiology remains unclear. This study aimed at exploring transcriptional profiles of broiler skeletal muscles exhibiting different WS severity to elucidate molecular mechanisms underlying the development and progression of WS. Total RNA was isolated from pectoralis major of male 7-week-old Ross 308 broilers. The samples were classified as mild (n = 6), moderate (n = 6), or severe (n = 4), based on number and thickness of the white striations on the meat surface. The transcriptome was profiled using a chicken gene expression microarray with one-color hybridization technique. Gene expression patterns of each WS severity level were compared against each other; hence, there were three comparisons: moderate vs. mild (C1), severe vs. moderate (C2), and severe vs. mild (C3). Differentially expressed genes (DEGs) were identified using the combined criteria of false discovery rate ≤ 0.05 and absolute fold change ≥1.2. Differential expression of 91, 136, and 294 transcripts were identified in C1, C2, and C3, respectively. There were no DEGs in common among the three comparisons. Based on pathway analysis, the enriched pathways of C1 were related with impaired homeostasis of macronutrients and small biochemical molecules with disrupted Ca2+-related pathways. Decreased abundance of the period circadian regulator suggested the shifted circadian phase when moderate WS developed. The enriched pathways uniquely obtained in C2 were RNA degradation, Ras signaling, cellular senescence, axon guidance, and salivary secretion. The DEGs identified in those pathways might play crucial roles in regulating cellular ion balances and cell-cycle arrest. In C3, the pathways responsible for phosphatidylinositol 3-kinase-Akt signaling, p53 activation, apoptosis, and hypoxia-induced processes were modified. Additionally, pathways associated with a variety of diseases with the DEGs involved in regulation of [Ca2+], collagen formation, microtubule-based motor, and immune response were identified. Eight pathways were common to all three comparisons (i.e., calcium signaling, Ras-associated protein 1 signaling, ubiquitin-mediated proteolysis, vascular smooth muscle contraction, oxytocin signaling, and pathway in cancer). The current findings support the role of intracellular ion imbalance, particularly Ca2+, oxidative stress, and impaired programmed cell death on WS progression.