Miracle-dz/UniFAR-FTUs huggingface dataset:
Escherichia coli “TatExpress” strains export several g/L human growth hormone to the periplasm by the Tat pathway

Escherichia coli is a heavily used platform for the production of biotherapeutic and other high‐value proteins, and a favored strategy is to export the protein of interest to the periplasm to simplify downstream processing and facilitate disulfide bond formation. The Sec pathway is the standard means of transporting the target protein but it is unable to transport complex or rapidly folding proteins because the Sec system can only transport proteins in an unfolded state. The Tat system also operates to transport proteins to the periplasm, and it has significant potential as an alternative means of recombinant protein production because it transports fully folded proteins. Here, we have tested the Tat system's full potential for the production of biotherapeutics for the first time using fed‐batch fermentation. We expressed human growth hormone (hGH) with a Tat signal peptide in E. coli W3110 “TatExpress” strains that contain elevated levels of the Tat apparatus. This construct contained four amino acids from TorA at the hGH N‐terminus as well as the initiation methionine from hGH, which is removed in vivo. We show that the protein is efficiently exported to the periplasm during extended fed‐batch fermentation, to the extent that it is by far the most abundant protein in the periplasm. The protein was shown to be homogeneous, disulfide bonded, and active. The bioassay showed that the yields of purified periplasmic hGH are 5.4 g/L culture whereas an enzyme‐linked immunosorbent assay gave a figure of 2.39 g/L. Separate analysis of a TorA signal peptide linked to hGH construct lacking any additional amino acids likewise showed efficient export to the periplasm, although yields were approximately two‐fold lower.
Simultaneous Detection of the T790M and L858R Mutations in the EGFR Gene by Oligoribonucleotide Interference-PCR

A de novo single-nucleotide mutation in the EGFR gene can cause the development of lung cancer. EGFR tyrosine kinase inhibitors (EGFR-TKIs) are used for clinical treatment of such lung cancers, but acquired resistance often mitigates their efficacy. Accordingly, monitoring of de novo and acquired nucleotide mutations is essential for clinical treatment of lung cancers with EGFR-TKIs. Previously, we reported that oligoribonucleotide interference-PCR (ORNi-PCR) can accurately and cost-effectively detect single-nucleotide mutations. In this study, we applied ORNi-PCR to simultaneous detection of the de novo L858R and acquired T790M mutations in the EGFR gene in lung cancer cells. First, we established optimal experimental conditions for ORNi-PCR to simultaneously detect the two single-nucleotide mutations in genomic DNA from lung cancer cells. The conditions we established could also be used for ORNi-PCR using complementary DNA reverse-transcribed from extracted RNA. We found that ORNi-PCR could detect lung cancer cells possessing both single-nucleotide mutations among a large number of cells harboring wild-type sequences, even when the cancer cells constituted less than ~0.2% of all cells. Our findings demonstrate that ORNi-PCR can simultaneously detect multiple single-nucleotide mutations in a gene of interest and might therefore be useful for simultaneous detection of EGFR mutations in clinical examinations.
Prevalence of Patellar Tendinopathy and Patellar Tendon Abnormality in Male Collegiate Basketball Players: A Cross-Sectional Study.

CONTEXT Patellar tendinopathy (PT) is a degenerative condition known to affect athletes who participate in sports like basketball and volleyball. Patellar tendinopathy is a challenging condition to treat and may cause an athlete to prematurely retire from sport. The prevalence of PT in male collegiate basketball players is unknown. OBJECTIVE To determine the prevalence of PT and patellar tendon abnormality (PTA) in a population of male collegiate basketball players. DESIGN Cross-sectional study. SETTING National Collegiate Athletic Association Divisions II and III, National Association of Intercollegiate Athletics, and Northwest Athletic Conference male collegiate basketball teams were assessed in a university laboratory setting. PATIENTS OR OTHER PARTICIPANTS Ninety-five male collegiate basketball players (age = 20.0 ± 1.7 years). MAIN OUTCOME MEASURE(S) A diagnostic ultrasound image of an athlete's patellar tendon was obtained from each knee. Patellar tendinopathy was identified based on a player's symptoms (pain with palpation) and the presence of a hypoechoic region on an ultrasonographic image. RESULTS A majority of participants, 53 of 95 (55.8%), did not present with pain during palpation or ultrasonographic evidence of PTA. Thirty-two basketball players (33.7%) displayed ultrasonographic evidence of PTA in at least 1 knee; 20 of those athletes (21.1%) had PT (pain and tendon abnormality). Nonstarters were 3.5 times more likely to present with PTA (odds ratio = 3.5, 95% confidence interval = 1.3, 9.6; P = .017) and 4 times more likely to present with PT (odds ratio = 4.0, 95% confidence interval = 1.1, 14.8; P = .038) at the start of the season. CONCLUSIONS One in 3 male collegiate basketball players presented with either PT or PTA. Sports medicine professionals should evaluate basketball athletes for PT and PTA as part of a preseason screening protocol.
EMG-Based Real-Time Linear-Nonlinear Cascade Regression Decoding of Shoulder, Elbow, and Wrist Movements in Able-Bodied Persons and Stroke Survivors

Objective: This study aimed to decode shoulder, elbow and wrist dynamic movements continuously and simultaneously based on multi-channel surface electromyography signals, useful for electromyography controlled exoskeleton robots for upper-limb rehabilitation. Methods: Ten able-bodied subjects and ten stroke subjects were instructed to voluntarily move the shoulder, elbow and wrist joints back and forth in a horizontal plane with an exoskeleton robot. The shoulder, elbow and wrist movements and surface electromyography signals from six muscles crossing the joints were recorded. A set of three parallel linear-nonlinear cascade decoders was developed to continuously estimate the selected shoulder, elbow and wrist movements based on a generalized linear model using the anterior deltoid, posterior deltoid, biceps brachii, long head triceps brachii, flexor carpi radialis, and extensor carpi radialis muscle electromyography signals as the model inputs. Results: The decoder performed well for both healthy and stroke populations. As movement smoothness decreased, decoding performance decreased for the stroke population. Conclusion: The proposed method is capable of simultaneously and continuously estimating multi-joint movements of the human arm in real-time by characterizing the nonlinear mappings between muscle activity and kinematic signals based on linear regression. Significance: This may prove useful in developing myoelectric controlled exoskeletons for motor rehabilitation of neurological disorders.
PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks

RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction. We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle. We also demonstrate the potential of PRAS for wide adoption by applying it to the enhanced CLIP-seq (eCLIP) datasets of 37 RNA decay related RBPs in two human cell lines. PRAS can be utilized to investigate any RBPs with available CLIP-seq peaks. PRAS is freely available at http://ouyanglab.jax. org/pras/.
Cistus incanus L. as an Innovative Functional Additive to Wheat Bread

Cistus incanus L. (CI) has been proposed as an innovative functional supplement of food products, and hence the present study aimed to evaluate the effect of the addition of dried CI on the properties of bread. Bread was prepared from white wheat flour supplemented with the addition of 1%, 2%, 3%, 4%, and 5% of ground CI. After the completion of baking process, various characteristics of the obtained bread product, such as yield, volume, porosity, acidity, color, and texture, were evaluated. In addition, total phenolic content (TPC), ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical scavenging activity, chelating power (CHEL), and ability to quench OH∙ radicals were measured. The results showed that the addition of CI to bread caused a reduction in the volume of bread, but texture of the crumbs was acceptable. Acidity and moisture content of bread were found to be increased following CI enrichment. Significant changes in the ash content and the color of bread crumbs were also observed. Bread incorporated with CI was characterized by significantly higher TPC and much higher antioxidant activity, as measured by ABTS, CHEL, and OH∙ radicals, compared to control bread. Supplementation of bread with 3% CI produced a product with desirable characteristics which was also favored by consumers.
The Pharmacoeconomic Analysis of Cetuximab and Panitumumab in the 1st Line Treatment of mCRC in Real Clinical Practice in the Czech Republic.

BACKGROUND The anti-epidermal growth factor receptor (EGFR) drugs cetuximab and panitumumab are currently reimbursed when administered during the first and subsequent lines of treatment of patients in the Czech Republic with metastatic colorectal cancer (mCRC). Because cetuximab and panitumumab do not show significant differences in efficacy, their choice may be dependent on cost. This retrospective study analyzed the costs of first-line treatment with cetuximab and panitumumab of patients with mCRC and wild type KRAS, as well as evaluated the correlations between costs and effectiveness, as determined by progression-free survival (PFS) and overall survival (OS). PATIENTS AND METHODS This analysis included 51 patients with mCRC and confirmed wild type KRAS treated at the comprehensive cancer centre in the Czech Republic between November 2011 and April 2018. Of these 51 patients, 22 were treated with cetuximab and 29 with panitumumab. Direct medical costs (medications, clinical examinations and procedures, and hospitalization) were evaluated from the initiation of treatment with anti-EGFR drug to disease progression and death. Mean follow-up was 21 months in the cetuximab group and 19 months in the panitumumab group. RESULTS Reimbursement for anti-EGFR drugs until disease progression accounted for 71% (mean, 964,288 CZK per patient) of total costs in the cetuximab group and 77% (mean, 1,003,229 CZK per patient) of total costs in the panitumumab group, with median PFS in these two groups being 10.7 months and 8.1 months, respectively. Reimbursement of expensive center drugs from the start of anti-EGFR treatment to patient death accounted for 55% of total costs in the cetuximab group (mean, 1,752,702 CZK per patient) and 63% of total costs in the panitumumab group (mean, 1,596,919 CZK per patient), with median OS in these two groups being 20.2 months and 19.8 months, respectively. No significant between-group differences in clinical effectiveness and costs of treatment were observed (p > 0.05 each). CONCLUSION Reimbursement for biological agents is the most expensive item in the first-line treatment of mCRC patients with wild type KRAS, both to disease progression and death. The clinical effectiveness and costs of cetuximab and panitumumab did not differ significantly. Supported by CZECRIN (identification code LM2015090); CZECRIN_4 PACIENTY (No. CZ.02.1.01/0.0/0.0/16_013/0001826). The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 30. 4. 2019 Accepted: 17. 6. 2019.
Distribution patterns of the cutaneous nerves on the dorsum of the foot and their clinical significance

The aim of this study was to clarify the distribution patterns of the cutaneous nerves on the dorsum of the foot. This study investigated 130 feet of 77 cadavers. The distribution patterns of the sural (SN) and deep fibular nerves (DFN) were classified into five and four types, respectively. In Type A, the SN was only distributed to the lateral side of the fifth toe. In Type B, the nerve was distributed to the medial side of the fourth toe and both sides of the fifth toe. In Type C, the nerve was mainly distributed to the lateral side of the fifth toe. In Type D, the nerve was distributed to the lateral side of the third toe and both sides of the fourth and fifth toes. In Type E, no SN was found. In Type α, the DFN was simultaneously distributed to the lateral side of the first toe and the medial side of the second toe. In Type β, the nerve was distributed like in Type α and additionally to the medial side of the first toe. In Type γ, the nerve was distributed like in Type α and additionally to the lateral side of the second toe and the medial side of the third toe. In Type δ, no DFN was found. The results of this study will help physicians to reduce the incidence of iatrogenic nerve injury and improve the quality of diagnoses of relevant nerves in this body region. Clin. Anat. 33:592–597, 2020. © 2019 Wiley Periodicals, Inc.
Thoracic epidural anaesthesia and analgesia ameliorates surgery-induced stress response and postoperative pain in patients undergoing radical oesophagectomy

Objective An acute severe stress response associated with major surgery can adversely affect the inflammatory and hormonal responses. We hypothesised that total intravenous anaesthesia (TIVA) combined with thoracic epidural anaesthesia and analgesia (TEA) attenuates the stress response and postoperative pain in patients undergoing radical oesophagectomy. Methods Forty patients scheduled for elective radical oesophagectomy were randomly assigned to one of two groups: TIVA or TIVA+TEA. The plasma levels of stress hormones and cytokines, consumption of fentanyl, postoperative visual analogue scale (VAS) scores within 48 hours, and extubation time were assessed. Results The plasma levels of interleukin-6, norepinephrine, cortisol, and adrenocorticotropic hormone at 3 hours after the beginning of surgery were significantly higher in the TIVA group than TIVA+TEA group. The plasma level of interleukin-10 at 3 hours after the beginning of surgery was significantly lower in the TIVA group than TIVA+TEA group. The consumption of fentanyl was significantly greater, VAS scores were significantly higher, and extubation time was significantly longer in the TIVA group than TIVA+TEA group. Conclusions The findings suggest that combination of TIVA and TEA may attenuate the intraoperative stress response and postoperative pain in patients undergoing radical oesophagectomy.
Component-Resolved Diagnosis in Food Allergies

Component-resolved diagnostics (CRD) in food allergies is an approach utilized to characterize the molecular components of each allergen involved in a specific IgE (sIgE)-mediated response. In the clinical practice, CRD can improve diagnostic accuracy and assist the physician in many aspects of the allergy work-up. CRD allows for discriminatory co-sensitization versus cross-sensitization phenomena and can be useful to stratify the clinical risk associated with a specific sensitization pattern, in addition to the oral food challenge (OFC). Despite this, there are still some unmet needs, such as the risk of over-prescribing unnecessary elimination diets and adrenaline auto-injectors. Moreover, up until now, none of the identified sIgE cutoff have shown a specificity and sensitivity profile as accurate as the OFC, which is the gold standard in diagnosing food allergies. In light of this, the aim of this review is to summarize the most relevant concepts in the field of CRD in food allergy and to provide a practical approach useful in clinical practice.
Effect of population stratification on SNP‐by‐environment interaction

Proportions of false‐positive rates in genome‐wide association analysis are affected by population stratification, and if it is not correctly adjusted, the statistical analysis can produce the large false‐negative finding. Therefore various approaches have been proposed to adjust such problems in genome‐wide association studies. However, in spite of its importance, a few studies have been conducted in genome‐wide single nucleotide polymorphism (SNP)‐by‐environment interaction studies. In this report, we illustrate in which scenarios can lead to the false‐positive rates in association mapping and approach to maintaining the overall type‐1 error rate.
A ten-year microbiological study of Pseudomonas aeruginosa strains revealed diffusion of carbapenems and quaternary ammonium compounds resistant populations

Pseudomonas aeruginosa is one of the leading causes of healthcare-associated infections. For this study, the susceptibility profiles to antipseudomonal antibiotics and a quaternary ammonium compound, didecyldimethylammonium chloride (DDAC), widely used as a disinfectant, were established for 180 selected human and environmental hospital strains isolated between 2011 and 2020. Furthermore, a genomic study was performed to determine their resistome and clonal putative relatedness. During the ten-year study period, it was estimated that 9.5% of clinical P. aeruginosa were resistant to carbapenem, 11.9% presented an MDR profile, and 0.7% an XDR. Decreased susceptibility (DS) to DDAC was observed for 28.0% of strains that was significantly more associated with MDR and XDR profiles and from hospital environmental samples (p <0.0001). According to genomic analyses, the P. aeruginosa population unsusceptible to carbapenems and/or to DDAC was diverse but mainly belonged to top ten high-risk clones described worldwide. The carbapenem resistance appeared mainly due to the production of the VIM-2 carbapenemase (39.3%) and DS to DDAC mediated by MexAB-OprM pump efflux overexpression. This study highlights the diversity of MDR/XDR populations of P. aeruginosa which are unsusceptible to molecules that are widely used in medicine and hospital disinfection and are probably distributed in hospitals worldwide.
A New Perspective on Dry Eye Classification: Proposal by the Asia Dry Eye Society

Abstract: The 2017 consensus report of the Asia Dry Eye Society (ADES) on the definition and diagnosis of dry eyes described dry eye disease as “Dry eye is a multifactorial disease characterized by unstable tear film causing a variety of symptoms and/or visual impairment, potentially accompanied by ocular surface damage. ” The report emphasized the instability of tear film and the importance of visual dysfunction in association with dry eyes, highlighting the importance of the evaluation of tear film stability. This report also discussed the concept of tear film–oriented therapy, which stemmed from the definition, and which is centered on provision of insufficient components in each tear film layer and ocular surface epithelium. The current ADES report proposes a simple classification of dry eyes based on the concept of tear film–oriented diagnosis and suggests that there are three types of dry eye: aqueous-deficient, decreased wettability, and increased evaporation. It is suggested that these three types respectively coincide with the problems of each layer: aqueous, membrane-associated mucins, and lipid/secretory mucin. Although each component cannot be quantitatively evaluated with the current technology, a practical diagnosis based on the patterns of fluorescein breakup is recommended. The Asia Dry Eye Society classification report suggests that for a practical use of the definition, diagnostic criteria and classification system should be integrated and be simple to use. The classification system proposed by ADES is a straightforward tool and simple to use, only through use of fluorescein, which is available even to non-dry eye specialists, and which is believed to contribute to an effective diagnosis and treatment of dry eyes.
Telomere Abnormalities in the Pathobiology of Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) occurs primarily in older adults and the incidence is clearly associated with aging. This disease seems to be associated with several hallmarks of aging, including telomere attrition and cellular senescence. Increasing evidence suggests that abnormalities involving telomeres and their proteome play a significant role in the pathobiology of IPF. The aim of this study is to summarize present knowledge in the field, as well as to discuss its possible clinical implications. Numerous mutations in genes associated with telomere functioning were studied in the context of IPF, mainly for Telomerase Reverse Transcriptase (TERT) and Telomerase RNA Component (TERC). Such mutations may lead to telomere shortening, which seems to increase the risk of IPF, negatively influence disease progression, and contribute to worse prognosis after lung transplantation. Some evidence indicates the possibility for the use of telomerase activators as potential therapeutic agents in pulmonary fibrosis. To sum up, increasing evidence suggests the role of telomere abnormalities in the pathobiology of IPF, natural history and prognosis of the disease. There are also possibilities for telomerase targeting in the potential development of new treatment agents. However, all these aspects require further research.
Feasibility study assessing equitable delivery of newborn pulse oximetry screening in New Zealand’s midwifery-led maternity setting

Objectives The aim of this study was to conduct New Zealand-specific research to inform the design of a pulse oximetry screening strategy that ensures equity of access for the New Zealand maternity population. Equity is an important consideration as the test has the potential to benefit some populations and socioeconomic groups more than others. Setting New Zealand has an ethnically diverse population and a midwifery-led maternity service. One quaternary hospital and urban primary birthing unit (Region A), two regional hospitals (Region B) and three regional primary birthing units (Region C) from three Health Boards in New Zealand’s North Island participated in a feasibility study of pulse oximetry screening. Home births in these regions were also included. Participants There were 27 172 infants that satisfied the inclusion criteria; 16 644 (61%) were screened. The following data were collected for all well newborn infants with a gestation age ≥35 weeks: date of birth, ethnicity, type of maternity care provider, deprivation index and screening status (yes/no). The study was conducted over a 2-year period from May 2016 to April 2018. Results Screening rates improved over time. Infants born in Region B (adjusted OR=0.75; 95% CI 0.67 to 0.83) and C (adjusted OR=0.29; 95% CI 0.27 to 0.32) were less likely to receive screening compared with those born in Region A. There were significant associations between screening rates and deprivation, ethnicity and maternity care provider. Lack of human and material resources prohibited universal access to screening. Conclusion A pulse oximetry screening programme that is sector-led is likely to perpetuate inequity. Screening programmes need to be designed so that resources are distributed in the way most likely to optimise health outcomes for infants born with cardiac anomalies. Ethics approval This study was approved by the Health and Disability Ethics Committees of New Zealand (15/NTA/168).