Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthetic Biology and Metabolic Engineering Employing Escherichia coli for C2–C6 Bioalcohol Production

Biofuel production from renewable and sustainable resources is playing an increasingly important role within the fuel industry. Among biofuels, bioethanol has been most widely used as an additive for gasoline. Higher alcohols can be blended at a higher volume compared to ethanol and generate lower greenhouse gas (GHG) emissions without a need to change current fuel infrastructures. Thus, these fuels have the potential to replace fossil fuels in support of more environmentally friendly processes. This review summarizes the efforts to enhance bioalcohol production in engineered Escherichia coli over the last 5 years and analyzes the current challenges for increasing productivities for industrial applications.
Early Activation of Myeloid-Derived Suppressor Cells Participate in Sepsis-Induced Immune Suppression via PD-L1/PD-1 Axis

Background: Myeloid derived suppressor cells (MDSCs) have been reported to keep elevating during sepsis. The current study was performed to investigate the immunosuppressive effect of MDSCs and their subsets with the underlying mechanisms. Methods: The immunosuppressive status was manifested by the apoptosis of splenocytes, quantity of T cells and PD-1 expression. The dynamics of quantity and PD-L1 level of MDSCs and the subsets were determined over time. The subset of MDSCs with high PD-L1 level was co-cultured with T cells to observe the suppressive effect. Results: Abdominal abscess was observed after 7 days post-sepsis. Five biomarkers related to organ functions were all significantly higher in the CLP group. The survival rate was consistent with the middle grade severity of sepsis model. Apoptosis of splenocytes increased over time during sepsis; CD4 + T cell decreased from day 1 post-sepsis; CD8+ T cells significantly reduced at day 7. The PD-1 expression in spleen was upregulated from an early stage of sepsis, and negatively related with the quantity of T cells. MDSCs were low at day 1 post-sepsis, but increased to a high level later; the dynamics of PMN-MDSC was similar to MDSCs. PD-L1 on MDSCs was highest at day 1 post-sepsis; PMN-MDSC was the main subset expressing PD-L1. The PMN-MDSC with high PD-L1 expression level extracted on day 1 after surgery from CLP mice significantly inhibited the proliferation of T cells. Conclusions: Sepsis-induced immunosuppression is initiated from a very early stage, a high expression level of PD-L1 on MDSCs and the main subset, PMN-MDSC might play a critical role suppressive role on T cells through PD-L1/PD-1 axis.
Predicting Cognitive Load and Operational Performance in a Simulated Marksmanship Task

Modern operational environments can place significant demands on a service member's cognitive resources, increasing the risk of errors or mishaps due to overburden. The ability to monitor cognitive burden and associated performance within operational environments is critical to improving mission readiness. As a key step toward a field-ready system, we developed a simulated marksmanship scenario with an embedded working memory task in an immersive virtual reality environment. As participants performed the marksmanship task, they were instructed to remember numbered targets and recall the sequence of those targets at the end of the trial. Low and high cognitive load conditions were defined as the recall of three- and six-digit strings, respectively. Physiological and behavioral signals recorded included speech, heart rate, breathing rate, and body movement. These features were input into a random forest classifier that significantly discriminated between the low- and high-cognitive load conditions (AUC = 0.94). Behavioral features of gait were the most informative, followed by features of speech. We also showed the capability to predict performance on the digit recall (AUC = 0.71) and marksmanship (AUC = 0.58) tasks. The experimental framework can be leveraged in future studies to quantify the interaction of other types of stressors and their impact on operational cognitive and physical performance.
SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response

The most severe and fatal infections with SARS-CoV-2 result in the acute respiratory distress syndrome, a clinical phenotype of coronavirus disease 2019 (COVID-19) that is associated with virions targeting the epithelium of the distal lung, particularly the facultative progenitors of this tissue, alveolar epithelial type 2 cells (AT2s). Little is known about the initial responses of human lung alveoli to SARS-CoV-2 infection due in part to inability to access these cells from patients, particularly at early stages of disease. Here we present an in vitro human model that simulates the initial apical infection of the distal lung epithelium with SARS-CoV-2, using AT2s that have been adapted to air-liquid interface culture after their derivation from induced pluripotent stem cells (iAT2s). We find that SARS-CoV-2 induces a rapid global transcriptomic change in infected iAT2s characterized by a shift to an inflammatory phenotype predominated by the secretion of cytokines encoded by NF-kB target genes, delayed epithelial interferon responses, and rapid loss of the mature lung alveolar epithelial program. Over time, infected iAT2s exhibit cellular toxicity that can result in the death of these key alveolar facultative progenitors, as is observed in vivo in COVID-19 lung autopsies. Importantly, drug testing using iAT2s confirmed an antiviral dose-response to remdesivir and demonstrated the efficacy of TMPRSS2 protease inhibition, validating a putative mechanism used for viral entry in human alveolar cells. Our model system reveals the cell-intrinsic responses of a key lung target cell to infection, providing a physiologically relevant platform for further drug development and facilitating a deeper understanding of COVID-19 pathogenesis.
Prospect of Stem Cell Therapy and Regenerative Medicine in Osteoporosis

The field of cell therapy and regenerative medicine can hold the promise of restoring normal tissues structure and function. Additionally, the main targets of stem cell-based therapies are chronic diseases and lifelong disabilities without definite cures such as osteoporosis. Osteoporosis as one of the important causes of morbidity in older men and post-menopausal women is characterized by reduced bone quantity or skeletal tissue atrophy that leads to an increased risk of osteoporotic fractures. The common therapeutic methods for osteoporosis only can prevent the loss of bone mass and recover the bone partially. Nevertheless, stem cell-based therapy is considered as a new approach to regenerate the bone tissue. Herein, mesenchymal stem cells as pivotal candidates for regenerative medicine purposes especially bone regeneration are the most common type of cells with anti-inflammatory, immune-privileged potential, and less ethical concerns than other types of stem cells which are investigated in osteoporosis. Based on several findings, the mesenchymal stem cells effectiveness near to a great extent depends on their secretory function. Indeed, they can be involved in the establishment of normal bone remodeling via initiation of specific molecular signaling pathways. Accordingly, the aim herein was to review the effects of stem cell-based therapies in osteoporosis.
Growth Response of Tapinanthus bangwensis (Engl. and Krause, Danser) Seeds in vitro and Artificial Infestation in the Field

The growth response of mistletoe, Tapinanthus bangwensis (Engl. and Krause) Danser to different temperatures and photoperiods on hormone-free culture media in vitro were assessed. Cultural procedure with plant sap extracts and field infestations were used to study the mistletoe interaction with Gliricidia sepium, Mangifera indica, Coffee robusta and Theobroma cacao. In the laboratory, mistletoe responded positively to a temperature range of 25-30 °C and 16-24 hr photoperiod. The seedling stages of germination, holdfast and haustorium development and leaf emergence were achieved optimally on an artificial medium of 1% (w/v) mineral salts and vitamins, 3% (w/v) sucrose, 1% (w/v) glucose, 0.04% (w/v) potassium nitrate (KNO3) and 1% (v/v) amino acid. Generally, growth was faster in field infestation than in vitro culture. Tapinanthus bangwensis did not develop on G. sepium branches and its extracts. This is consistent with field observations where mistletoes were not found on G. sepium. The selective nature of T. bangwensis to develop on different hosts and their extracts reflects differences in biochemical/nutrient contents of hosts sap. However, it was more probable that physical destruction of M. indica cambial cylinder by mistletoe haustorium deprived the parasite of water and nutrients resulting in its death. Based on T. bangwensis growth responses in nature and in culture, T. cacao was found susceptible, C. robusta was moderately susceptible and G. sepium and M. indica was non-hosts.
Spatial variability of soil enzymes in a sinkhole undergoing forage transition.

Tall fescue is a dominant forage grass in the southeastern United States. The dominant fescue cultivar, KY 31, is infected with an alkaloid&producing endophyt e, and research is evaluating new forage species and endophyte&free cultivars as pasture replacements. S patial distribution of soil enzymes affecting soil processes in transitional forage systems is not well&studied. We evaluated the spatial variability of soil enzymes involved in C metabolism at a sinkhole site in central Kentucky, USA. Dehydrogenase and β&glucosidase were selected because they reflect soil microbiological activity status and play a key role in bioprocesses involving C cycling. There was evidence of spatial variability for enzyme activity across the sinkhole. Dehydrogenase activity showed moderate spatial structure at 15&30 cm depth compared to strong spatial structure over a 100 m range under endophyte&infect ed KYFA9301/A584 and KY31. There was moderate spatial correlation over a 60 m range under endophyte&free KYFA9301, and a complete nugget effect unde r the undisturbed control. Spatial analysis of β&glucosidase activity indicated a weak to moderate spatial structure over a 40 to 100 m range under different forage species, except for a pure nugget at 15&30 c under KY31 and KYFA9301/A584. Spatial cross correlation analysis showed that both enzymes are spatially correlated for two soil depths over a range from 10 to 30 m. Cross semivariance analysis showed spatial independence between soil enzyme activity and TN, soil pH, and clay content.
Example-based Exploration: Exploring Knowledge through Examples

Exploration is one of the primordial ways to accrue knowledge about the world and its nature. As we accumulate, mostly automatically, data at unprecedented volumes and speed, our datasets have become complex and hard to understand. In this context, exploratory search provides a handy tool to progressively gather the necessary knowledge by starting from a tentative query that can provide cues about the next queries to issue. An exploratory query should be simple enough to avoid complicate declarative languages (such as SQL or SPARQL) and convoluted mechanism, and at the same time retain the flexibility and expressiveness required to express complex information needs. Recently, we have witnessed a rediscovery of the so called example-based methods , in which the user, or the analyst circumvent query languages by using examples as input. This shift in semantics has led to a number of methods receiving as query a set of example members of the answer set. The search system then infers the entire answer set based on the given examples and any additional information provided by the underlying database. In this tutorial, we present an excursus over the main example-based methods for exploratory analysis. We show how different data types require different techniques, and present algorithms that are specifically designed for relational, textual, and graph data. We conclude by providing a unifying view of this query-paradigm and identify new exciting research directions.
EFFECT OF EXOGENOUS APPLICATION OF SALICYLIC ACID AND SODIUM NITROPRUSSIDE ON MAIZE UNDER SELENIUM STRESS

With the development of industry, there has been an impressive increment in the release of mechanical waste to the environment, mostly soil and water, which has prompted the accretion of heavy metals, especially in urban regions (Dixit et al., 2015). These metals also initiate severe health problems due to transference of these pollutants into the food chain. Due to extreme utilization of chemicals and varying environmental conditions; heavy metals are being accrued in the soil and cause serious health problems and danger to human life (Jeelani et al., 2017; Ahsan et al., 2018a,b; Sattar et al., 2019). Selenium (Se) is normally present in nature that is randomly dispersed in the outer layer of the earth (0.05 mg kg) (Kabata-Pendias and Szteke, 2015). In agriculture, Se is utilized as an expansion, mostly as sodium selenite to bug sprays, composts and foliar showers. Moreover, several livestock foodstuffs are encouraged with this element. It is comparatively communal of different makeups and medicines, as a tonic (Kabata-Pendias, 2011). Due to its semi-conductive possessions, selenium is extensively used in manufacturing electrical things. It is also released from metallurgical processes and largely used in glass manufacturing, dyes, greasing oil, dyestuffs, food supplements, farmed products etc. (Bodnar et al., 2012; Mehdi et al., 2013). Metal stress is one of the serious problems throughout the world, affecting the metabolic responses of crops, human health and the environment (Deinlein et al., 2014). Selenium at higher levels is viewed as harmful to the plants (Germ et al., 2007). Hence, in the plants developing in soils having poisonous convergences of Se, different impacts, for example, chlorosis, senescence, diminished development, and potential yield (Zhang et al., 2007) have been accounted for. A range of chemicals is presently utilized on plants existing in stress environments, and in many cases, remarkable results have appeared (Farooq et al., 2009). Utilization of plant growth regulators (PGRs) is a favourable method to expand the resistance against abiotic stresses (Ali et al., 2013). Without a doubt, plant weight increases due to various PGRs (El-Tayeb, 2005). Salicylic acid (SA) is a growth controller of phenolic nature, which play a role in plant protection from environmental hassle (Karlidag et al., 2009). It enhances germination, development, gas exchange parameters and particle take-up (He et al., 2010). Moreover, it is currently certain that the SA gives security against various abiotic stresses (Karlidag et al., 2009, El-Tayeb, 2005). SA has been accounted for to Pak. J. Agri. Sci., Vol. 57(1), 150-158;2020 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: 10.21162/PAKJAS/20.8562 http://www.pakjas. com.pk
Modeling and Control of Underactuated Three-Dimensional Overhead Crane Systems

Overhead crane systems play a vital role in different factories to transport heavy loads. This paper provides an overview of recent developments in the modeling and control of three-dimensional overhead crane systems. It provides a categorized survey of the published work. Different control methodologies when applied to overhead crane are examined, outlined and assessed to aid for future work.
CDH1 mutations in gastric cancers are not influenced by family history

Background: CDH1 mutation is the most frequent genetic alteration in hereditary diffuse gastric cancer (GC) and early onset diffuse GC patients. However, the incidence of CDH1 mutations in sporadic GC with or without family history has not been studied. Methods: This retrospective study includes a total of 993 Korean patients with primary advanced GC who underwent surgery and received palliative chemotherapy. Targeted deep sequencing was performed in all cases and family history of GC was searched with survival analysis. Results: We found CDH1 alterations in 146 of 993 patients (14.7%) and 8 were germline (0.8%). Out of 146 patients with CDH1 mutations, 25 (17.1%) had a family history of GC in one of their first relatives, and 12 patients (8.2%) were diagnosed with familial GC (FGC). All cases with FGC were diffuse type by Lauren classification, and only one harbored a previously reported germline mutation of CDH1 (c.2638G>A) and the remaining 11 harbored known somatic CDH1 mutations. Among all patients with CDH1 mutation, there was no significant survival difference between patients with family history or FGC. In the 847 patients without CDH1 mutation, 189 (22.3 %) had a family history of GC and 92 patients (10.9%) were FGC. CDH1 mutations were more frequent in patients with early onset (<45 years) GC (45.5%) compared with patients with late onset GC (10.9%) (p = 0.001), but were not significantly associated with the family history of GC (p > 0.05). Conclusions: CDH1 mutations are mostly somatic and typically are not associated with family history.
Phylogenetic Analyses and a Method for Rapid Molecular Diagnosis of Two Sunflower Seed Weevils (Coleoptera: Curculionidae)

Abstract The red sunflower seed weevil, Smicronyx fulvus LeConte, and gray sunflower seed weevil, Smicronyx sordidus LeConte (Coleoptera: Curculionidae), are among the most important seed pests of cultivated sunflowers, Helianthus annuus L. , in the northern Great Plains. A portion of 18S ribosomal DNA (18S rDNA) sequence from specimens of 31 populations of the morphologically similar species that were collected across a wide geographic region of the United States showed a consistent separation of the two species. The restriction endonuclease HaeII digests the piece of 18S rDNA in only one of the two species, and this restriction fragment-length polymorphism can be used for species diagnosis. Phylogenetic analysis for species of four tribes of the weevil subfamily Erirhininae showed that the sunflower seed weevil tribe, Smicronychini, is monophyletic.
Performance of Ultrasonography Compared to Conventional Radiography for the Diagnosis of Osteoarthritis in Patients With Knee Pain

Purpose: To investigate the performance of ultrasonography (US) for the detection of knee osteoarthritis (OA) in patients suffering from knee pain, compared to conventional radiographs. Methods: Cross-sectional study performed at a university teaching hospital. Consecutive patients complaining of unilateral or bilateral mechanical knee pain who signed an informed consent were included. All patients underwent simultaneously an ultrasonographic and a radiographic evaluation of the knee. Exclusion criteria were age under 18 years, prior diagnosis of knee OA, diagnosis of inflammatory arthritis, history of knee surgery or trauma, severe knee deformities, and corticosteroid injection within the last 2 months. The diagnostic properties of US for the detection of knee OA were evaluated using radiological data as the reference method. Evaluated test properties were sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and the positive and negative likelihood ratio (LR+ and LR–). Results: Three-hundred twenty-two knees (281 patients) were included. Radiographic degenerative changes were present in 56.8% (183) of the evaluated knees. Regarding the diagnostic properties of the US, the presence of either osteophytes or the compromise of the femoral hyaline cartilage had the best sensitivity to detect OA (95%), with a NPV of 92% and a LR– of 0,07, while the combined identification of osteophytes and compromise of the femoral hyaline cartilage had the best specificity (94%), with 94% PPV and a LR+ of 13. Conclusion: US demonstrated an excellent sensitivity with an adequate specificity for the detection of radiographic knee OA.
PISD CRISPR/Cas9 KO Plasmid (h): sc- 404398

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas9) system is an adaptive immune response defense mechanism used by archea and bacteria for the degradation of foreign genetic material (4,6). This mechanism can be repurposed for other functions, including genomic engineering for mammalian systems, such as gene knockout (KO) (1,2,3,5). CRISPR/Cas9 KO Plasmid products enable the identification and cleavage of specific genes by utilizing guide RNA (gRNA) sequences derived from the Genome-scale CRISPR Knock-Out (GeCKO) v2 library developed in the Zhang Laboratory at the Broad Institute (3,5).
K26 Antigen from L. infantum Mon1: Sequence Based Function-Localization Analysis

Visceral leishmaniasis (VL), a vector-borne disease caused by the Leishmania donovani complex, is a zoonotic disease. Annual incidence is estimated at 500,000 cases. Ninety percent of VL cases occur in just five countries: Bangladesh, India, Nepal, Sudan and Brazil. Overall prevalence is 12 million people and 350 million people are at risk for the disease. Leishmania K26 protein, which has a 14 amino acid repeat region, has been evaluated as an immunoresponsive diagnostic marker that might be more reliable than K36 or other candidates. In order to develop serological diagnosis, some investigations were conducted to evaluate the immunogenic properties of K26, but there are no data about its function or cellular localization (1-5). Therefore, secondary structure prediction, protein motifs based comparison as well as conserved regions, molecular electrostatic potential and possible location of the protein were used to predict a closely related function and cellular location for K26 protein.
Assessment and Comparison of the Efficacy of Methotrexate, Prednisolone, Adalimumab, and Tocilizumab on Multipotency of Mesenchymal Stem Cells

Mesenchymal stem cell (MSC)–based articular regeneration might be beneficial for both protecting and rebuilding cartilaginous tissues in the management of rheumatoid arthritis. However, it is unclear how current immunosuppressive strategies influence the multipotency of MSCs. The present study was undertaken to profile the direct effectiveness of major antirheumatic drugs including methotrexate, prednisolone, adalimumab, and tocilizumab on the multipotency of MSCs, with a special focus on chondrogenesis. The inhibitory effects of methotrexate on adipogenesis, osteogenesis, and chondrogenesis were observed to occur in a dose-dependent manner in an in vitro differentiation system. Prednisolone enhanced adipogenesis, but reduced alkaline phosphatase activity in osteoprogenitors and suppressed the formation of chondrospheroids. Adalimumab suppressed alkaline phosphatase activity, while tocilizumab diminished osteogenesis and chondrogenesis of MSCs in vitro. Chondrogenesis of antirheumatic drug-treated MSCs was also evaluated in vivo using a scaffolded spheroid-engrafted murine model. The biologics examined appeared to be relatively safe for cartilaginous formation, but methotrexate and prednisolone exhibited opposing influences on chondrogenesis. Taken together, these results reveal the direct efficacy of major antirheumatic agents on the multipotency of MSCs. Therefore, our findings suggest that optimization of medication protocols is further required for therapeutic approaches involving cartilaginous tissue engineering.