Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant Disease Classification: A Comparative Evaluation of Convolutional Neural Networks and Deep Learning Optimizers

Recently, plant disease classification has been done by various state-of-the-art deep learning (DL) architectures on the publicly available/author generated datasets. This research proposed the deep learning-based comparative evaluation for the classification of plant disease in two steps. Firstly, the best convolutional neural network (CNN) was obtained by conducting a comparative analysis among well-known CNN architectures along with modified and cascaded/hybrid versions of some of the DL models proposed in the recent researches. Secondly, the performance of the best-obtained model was attempted to improve by training through various deep learning optimizers. The comparison between various CNNs was based on performance metrics such as validation accuracy/loss, F1-score, and the required number of epochs. All the selected DL architectures were trained in the PlantVillage dataset which contains 26 different diseases belonging to 14 respective plant species. Keras with TensorFlow backend was used to train deep learning architectures. It is concluded that the Xception architecture trained with the Adam optimizer attained the highest validation accuracy and F1-score of 99.81% and 0.9978 respectively which is comparatively better than the previous approaches and it proves the novelty of the work. Therefore, the method proposed in this research can be applied to other agricultural applications for transparent detection and classification purposes.
Analysis of anaphase inhibitors in fission yeast

The spindle checkpoint monitors the metaphase to anaphase transition and delays cell cycle progression in the case of improper microtubule-kinetochore attachment. As a result of checkpoint activation, a signalling cascade is initiated and a number of complexes between the checkpoint components are formed. This leads to the inhibition of the Anaphase Promoting ComplexlCyclosome (APC/C), which is the ubiquitin ligase responsible for targeting mitotic proteins: securin and cyclin B for degradation by the 26S proteasome. The complexes formed include the MCC, or Mitotic Checkpoint Complex, which in fission yeast (Schizosaccharomyces pombe) consists of Mad2, Mad3 checkpoint proteins together with the APC/C activator, Slpl (the Cdc20 homologue). The MCC has been shown to bind and inhibit the APC/C in HeLa cells. In my PhD I focused on the interactions between the MCC and the APCIC, in particular on Mad3 protein. Mad3 is a conserved checkpoint component, homologous to human BubRl. It carries 2 putative KEN boxes, motifs, which typically target proteins for degradation (like D-boxes). I used mutated versions of the both KEN boxes in S. pombe Mad3 and showed that they are essential for Mad3 checkpoint function. One of the two motifs is also required for MCC formation, MCC-APC/C binding and Mad3 turnover in Gi stage of cell cycle. I argue that KEN boxes mediate the inhibitory interactions between checkpoint proteins and the APCIC. The formation of the MCC requires Mad2 and Mad3. These proteins are also dependent on one another for binding to the APC/C. I study the formation of the MCC, as well as its binding to the APC/C in different checkpoint mutants, trying to understand dependencies between these proteins and the requirement for kinetochore localisation. Finally, I make an attempt to study the cellular localisation of Slpl and the APC/C and find that while Sipi co-localises with a kinetochore marker, the APCIC subunits Cut9 and Lidl remain distributed around the fission yeast nucleus.
Prognostic Role of Demographic, Injury and Claim Factors in Disabling Pain and Mental Health Conditions 12 Months after Compensable Injury

Identifying who might develop disabling pain or poor mental health after injury is a high priority so that healthcare providers can provide targeted preventive interventions. This retrospective cohort study aimed to identify predictors of disabling pain or probable mental health conditions at 12 months post-injury. Participants were recruited 12-months after admission to a major trauma service for a compensable transport or workplace injury (n = 157). Injury, compensation claim, health services and medication information were obtained from the Victorian Orthopaedic Trauma Outcome Registry, Victorian State Trauma Registry and Compensation Research Database. Participants completed questionnaires about pain, and mental health (anxiety, depression, posttraumatic stress disorder) at 12 months post-injury. One third had disabling pain, one third had at least one probable mental health condition and more than one in five had both disabling pain and a mental health condition at 12 months post-injury. Multivariable logistic regression found mental health treatment 3–6 months post-injury, persistent work disability and opioid use at 6–12 months predicted disabling pain at 12 months post-injury. The presence of opioid use at 3–6 months, work disability and psychotropic medications at 6–12 months predicted a mental health condition at 12 months post-injury. These factors could be used to identify at risk of developing disabling pain who could benefit from timely interventions to better manage both pain and mental health post-injury. Implications for healthcare and compensation system are discussed.
Contrasting Immunomodulatory Effects of Probiotic and Pathogenic Bacteria on Eastern Oyster, Crassostrea Virginica, Larvae

Several Vibrio spp. cause acute and severe mortality events in hatcheries where larvae of bivalve mollusks are reared, potentially leading to subsequent shortage of bivalve seed for the grow-out industry. In particular, strains of Vibrio coralliilyticus have been identified as a major cause of disease in Pacific, Crassostrea gigas, and eastern, C. virginica, oyster hatcheries in the USA of America. Probiotic bacteria are an inexpensive, practical, and natural method of disease control. Previous research shows that pretreatment of larval oysters with probiotic bacteria Bacillus pumilus RI06–95 (RI) and Phaeobacter inhibens S4 (S4) significantly decreases mortality caused by experimental challenge with the bacterial pathogen V. coralliilyticus RE22 (RE22). This study aims to characterize the immune response of 6–10-day-old eastern oyster larvae to experimental challenge with pathogen V. coralliilyticus RE22 and probionts RI and S4. Treatments included (a) pathogen and probiont exposure at a concentration of 5 × 104 CFU per mL (~2500 bacterial cells per larva) for a duration of 6 h, (b) probiont exposure at the same concentration for a duration of 24 h, and (c) probiont RI daily treatment of larvae in the hatchery for 4, 11, and 15 days. Differential gene expression analysis compared pathogen or probiotic-treated transcriptomes to unexposed controls. Probiotic and pathogen treatment led to upregulation of transcripts coding for several immune pattern recognition receptors (PRRs) involved in environmental sensing and detection of microbes in oyster larvae. Larval oyster responses to pathogen RE22 suggested suppression of expression of genes in immune signaling pathways (myd88, tak1, nkap), failure in upregulation of immune effector genes, high metabolic demand, and oxidative stress that potentially contributed to mortality. On the other hand, the transcriptomic response to probiotic bacteria RI and S4 suggested activation of immune signaling pathways and expression of immune effectors (e.g., Cv-spi2, mucins and perforin-2). These key features of the host immune response to probiotic bacteria were shared despite the length of probiotic exposure, probiotic species, and the type of environment in which exposures were conducted. This study suggests that pre-exposure of eastern oyster larvae to probiotics for 6–24 h prior to pathogenic challenge leads to a robust and effective immune response that may contribute to protecting larvae from subsequent challenge with V. coralliilyticus RE22. This research provides new insights into host-microbe interactions in larval oysters that could be applied in the management of vibriosis in bivalve hatcheries.
Improving Influenza HA-Vlps Production in Insect High Five Cells via Adaptive Laboratory Evolution

The use of non-standard culture conditions has proven efficient to increase cell performance and recombinant protein production in different cell hosts. However, the establishment of high-producing cell populations through adaptive laboratory evolution (ALE) has been poorly explored, in particular for insect cells. In this study, insect High Five cells were successfully adapted to grow at a neutral culture pH (7.0) through ALE for an improved production of influenza hemagglutinin (HA)-displaying virus-like particles (VLPs). A stepwise approach was used for the adaptation process, in which the culture pH gradually increased from standard 6.2 to 7.0 (ΔPh = 0.2–0.3), and cells were maintained at each pH value for 2–3 weeks until a constant growth rate and a cell viability over 95% were observed. These adapted cells enabled an increase in cell-specific HA productivity up to three-fold and volumetric HA titer of up to four-fold as compared to non-adapted cells. Of note, the adaptation process is the element driving increased specific HA productivity as a pH shift alone was inefficient at improving productivities. The production of HA-VLPs in adapted cells was successfully demonstrated at the bioreactor scale. The produced HA-VLPs show the typical size and morphology of influenza VLPs, thus confirming the null impact of the adaptation process and neutral culture pH on the quality of HA-VLPs produced. This work strengthens the potential of ALE as a bioprocess engineering strategy to improve the production of influenza HA-VLPs in insect High Five cells.
Mental distress among U.S. adults during the COVID‐19 pandemic

Abstract Objective This study aims to document the impact of the COVID‐19 pandemic on mental health. Method We compared a nationally representative online sample of 2,032 U.S. adults in late April 2020 to 19,330 U.S. adult internet users who participated in the 2018 National Health Interview Survey (NHIS) using the Kessler‐6 scale of mental distress in the last 30 days. Results Compared to the 2018 NHIS sample, U.S. adults in April 2020 were eight times more likely to fit criteria for serious mental distress (27.7% vs. 3.4%) and three times more likely to fit criteria for moderate or serious mental distress (70.4% vs. 22.0%). Differences between the 2018 and 2020 samples appeared across all demographic groups, with larger differences among younger adults and those with children in the household. Conclusions These considerable levels of mental distress may portend substantial increases in diagnosed mental disorders and in their associated morbidity and mortality.
Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents

Abstract Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.
Anterior Lumbar Interbody Fusion With Cage Retrieval for the Treatment of Pseudarthrosis After Transforaminal Lumbar Interbody Fusion: A Single-Institution Case Series.

BACKGROUND The treatment of pseudarthrosis after transforaminal lumbar interbody fusion (TLIF) can be challenging, particularly when anterior column reconstruction is required. There are limited data on TLIF cage removal through an anterior approach. OBJECTIVE To assess the safety and efficacy of anterior lumbar interbody fusion (ALIF) as a treatment for pseudarthrosis after TLIF. METHODS ALIFs performed at a single academic medical center were reviewed to identify cases performed for the treatment of pseudarthrosis after TLIF. Patient demographics, surgical characteristics, perioperative complications, and 1-yr radiographic data were collected. RESULTS A total of 84 patients were identified with mean age of 59 yr and 37 women (44.0%). A total of 16 patients (19.0%) underwent removal of 2 interbody cages for a total of 99 implants removed with distribution as follows: 1 L2/3 (0.9%), 6 L3/4 (5.7%), 37 L4/5 (41.5%), and 55 L5/S1 (51.9%). There were 2 intraoperative venous injuries (2.4%) and postoperative complications were as follows: 7 ileus (8.3%), 5 wound-related (6.0%), 1 rectus hematoma (1.1%), and 12 medical complications (14.3%), including 6 pulmonary (7.1%), 3 cardiac (3.6%), and 6 urinary tract infections (7.1%). Among 58 patients with at least 1-yr follow-up, 56 (96.6%) had solid fusion. There were 5 cases of subsidence (6.0%), none of which required surgical revision. Two patients (2.4%) required additional surgery at the level of ALIF for pseudarthrosis. CONCLUSION ALIF is a safe and effective technique for the treatment of TLIF cage pseudarthrosis with a favorable risk profile.
Analysis the diurnal dynamic of photosynthetic characteristics and its influencing factors on Arundo donax var. versicolor

To uncover the diurnal dynamic character of photosynthesis and its impacting factors of Arundo donax var.versicolor in ecological ditch,net photosynthetic rate(Pn),photosynthetically active radiation(PAR),stomatal conductance(Gs),intercellular carbon dioxide concentration(Ci),leaf temperature(Tl),atmospheric temperature around the leaves(Ta) and transpiration rate(Tr) were measured in clear days using portable photosynthetic system(the model type is CID–340). The results showed: ①The diurnal Pn curve of Arundo donax var.versicolor presented a single-peak,which occurred at about 3 pm with a value of 19.76 μmol/(m2.s). ②Results of stepwise regression indicated that Tr,Ci,Tl and Ta took an important effect on Pn. ③Results of partial correlation analysis and path analysis indicated that Ci and Tr were two important factors influencing to Pn,and Ci had larger impact on Pn in comparison with Tr.
Tracking the Distribution and Burst of Nuclear Mitochondrial DNA Sequences (NUMTs) in Fig Wasp Genomes

Simple Summary Nuclear mitochondrial DNA sequences (NUMTs), which result from the insertion of exogenous mtDNA into the nuclear genome, are widely distributed in eukaryotes. However, how NUMTs are inserted into the nuclear genome and their post-insertion fates remain a mystery. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, which will be helpful to study the biological issues of NUMTs. We here select 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results show that the distributions of NUMTs are species- or lineage-specific. Furthermore, genomic environmental factors such as genome size, the damage-prone regions, and the mode of TE dynamics can determine the insertion and post-insertion fate of NUMTs. Especially because of TEs, the fragmentation and duplication of NUMTs, and thus their burst, are common. This is a relatively comprehensive investigation of the specific distribution of NUMTs and its influencing factors. Our study will help people to understand the evolution of exogenous fragments in the nuclear genome. Abstract Mitochondrial DNA sequences can be transferred into the nuclear genome, giving rise to nuclear mitochondrial DNA sequences (NUMTs). NUMTs have been described in numerous eukaryotes. However, the studies on the distribution of NUMTs and its influencing factors are still inadequate and even controversial. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, in which we selected 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results showed that the contents of NUMTs varied greatly in these species, and bursts of NUMTs existed in some species or lineages. Further detailed analyses showed that the large number of NUMTs might be related to the large genomes; NUMTs tended to be inserted into unstable regions of the genomes; and the inserted NUMTs might also be affected by transposable elements (TEs) in the neighbors, leading to fragmentations and duplications, followed by bursts of NUMTs. In summary, our results suggest that a variety of genomic environmental factors can determine the insertion and post-insertion fate of NUMTs, resulting in their species- or lineage-specific distribution patterns, and that studying the evolution of NUMTs can provide good evidence and theoretical basis for exploring the dynamics of exogenous DNA entering into the nuclear genome.
Estimating weekly excess mortality at sub-national level in Italy during the COVID-19 pandemic

In this study we present the first comprehensive analysis of the spatio-temporal differences in excess mortality during the COVID-19 pandemic in Italy. We used a population-based design on all-cause mortality data, for the 7,904 Italian municipalities. We estimated sex-specific weekly mortality rates for each municipality, based on the first four months of 2016–2019, while adjusting for age, localised temporal trends and the effect of temperature. Then, we predicted all-cause weekly deaths and mortality rates at municipality level for the same period in 2020, based on the modelled spatio-temporal trends. Lombardia showed higher mortality rates than expected from the end of February, with 23,946 (23,013 to 24,786) total excess deaths. North-West and North-East regions showed one week lag, with higher mortality from the beginning of March and 6,942 (6,142 to 7,667) and 8,033 (7,061 to 9,044) total excess deaths respectively. We observed marked geographical differences also at municipality level. For males, the city of Bergamo (Lombardia) showed the largest percent excess, 88.9% (81.9% to 95.2%), at the peak of the pandemic. An excess of 84.2% (73.8% to 93.4%) was also estimated at the same time for males in the city of Pesaro (Central Italy), in stark contrast with the rest of the region, which does not show evidence of excess deaths. We provided a fully probabilistic analysis of excess mortality during the COVID-19 pandemic at sub-national level, suggesting a differential direct and indirect effect in space and time. Our model can be used to help policy-makers target measures locally to contain the burden on the health-care system as well as reducing social and economic consequences. Additionally, this framework can be used for real-time mortality surveillance, continuous monitoring of local temporal trends and to flag where and when mortality rates deviate from the expected range, which might suggest a second wave of the pandemic.
The Noninvasive Diagnostic Value of MRN for CIDP: A Research from Qualitative to Quantitative

The MRN can be used to distinguish thickened nerve roots peripheral neuropathies and nonthickened nerve roots peripheral neuropathies. We found the MRN of either the brachial plexus or the lumbosacral plexus has a high diagnostic accuracy for CIDP, and the combined examination does not significantly improve diagnostic accuracy.
Dominant immune response to HLA‐B57/B58 molecules after platelet transfusion

Patients with hematologic malignancies require prophylactic or curative platelet transfusions to prevent or treat bleeding. Treatments such as chemotherapy, radiotherapy, and hematopoietic stem cell transplantation cause persistent thrombocytopenia, necessitating platelet transfusions. However, class I HLA antibodies can cause a serious complication: immune‐mediated platelet refractoriness. The mechanisms of alloimmunization are incompletely understood. We explored the immunogenicity of HLA molecules and the phenotype of the HLA‐specific CD4+ T cells involved in alloimmunization.
Polymorphism of murine endogenous proviruses revealed by using virus class-specific oligonucleotide probes

Inbred mice contain three classes of endogenous nonecotropic murine leukemia virus-related sequences, namely xenotropic, polytropic, and modified polytropic proviruses. Oligonucleotide probes specific for the three different classes were prepared and used to examine the diversity of endogenous sequences present in eight different strains of mice: HRS/J, BALB/cJ, A/J, AKR/J, C57BL/6J, DBA/2J, C57L/J, and C3H/HeJ. A high degree of polymorphism was observed. Overall, the strains showed between 17% (A/J and HRS/J) and 65% (C57BL/6J and C57L/J) shared proviruses, and only four proviruses were present in all eight strains. The similarity among the strains is due in part to the few proviruses present in all of the strains but also represents the independent assortment of a limited set of proviruses. These oligonucleotides provide a basis for determining the stability, distribution, and mutagenic potential of nonecotropic proviruses within the mouse genome.
Technology in education : looking toward 2020

Contents: J.L. Schwartz, C.L. Thompson, Foreword. P.P. Zodhiates, Preface. R.S. Nickerson, Technology in Education in 2020: Thinking About the Not-Distant Future. T.K. Landauer, Education in a World of Omnipotent and Omniscient Technology. H.E. Gardner, Mobilizing Resources for Individual-Centered Education. A. DiSessa, What Will It Mean to be "Educated" in 2020? A.H. Schoenfeld, Mathematics, Technology, and Higher-Order Thinking. W. Feurzeig, Apprentice Tools: Students as Practitioners. E. Soloway, It's 2020: Do You Know What Your Children are Learning in Programming Class? L.B. Resnick, A. Johnson, Intelligent Machines for Intelligent People: Cognitive Theory and the Future of Computer-Assisted Learning. R.D. Pea, Putting Knowledge to Use. S. M. Malcom, Technology in 2020: Educating a Diverse Population. D.K. Cohen, Educational Technology and School Organization. J. Minstrell, Teachers' Assistants: What Could Technology Make Feasible? W.H. Bossert, The Use of Technology to Improve Two Key Classroom Relationships. R.S. Nickerson, Summary.