Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes.

Coleoid cephalopods possess numerous complex, species-specific morphological and behavioural adaptations, e.g., a uniquely structured nervous system that is the largest among the invertebrates. The Hawaiian bobtail squid (Euprymna scolopes) is one of the most established cephalopod species. With its recent publication of the chromosomal-scale genome assembly and regulatory genomic data, it also emerges as a key model for cephalopod gene regulation and evolution. However, the latest genome assembly has been lacking a native gene model set. Our manuscript describes the generation of new long-read transcriptomic data and, made using this combined with a plethora of publicly available transcriptomic and protein sequence data, a new reference annotation for E. scolopes.

The effect of mirror therapy in the rehabilitation of flexor tendon injuries after primary surgical repair.

OBJECTIVE: The aim of this study was to evaluate the effectiveness of mirror therapy and to provide a clinical basis for better functional recovery in the rehabilitation of patients with flexor tendon injury. MATERIALS AND METHODS: Thirty patients were included and randomly divided between two groups: mirror therapy and conventional treatment. A physical therapy program consisting of whirlpool, ultrasound and transcutaneous electrical nerve stimulation was applied to both groups. In the mirror therapy group, flexor tendon gliding, blocking exercises, joint range of motion and resistance exercises were performed with the healthy hand via a mirror. In the conventional treatment group, the same exercises were performed with the affected hand without mirror. This treatment was continued for 12 sessions over 4 weeks. Joint range of motion, handgrip strength, pain, functionality, dexterity and kinesiophobia were evaluated before and after treatment. RESULTS: More improvement was observed in the mirror therapy group in terms of pain on visual analog scale, Patient-Rated Wrist Evaluation, Hand Function Index and Disabilities of the Arm, Shoulder and Hand scores (p = 0.025, p = 0.004, p < 0.001 and p < 0.001, respectively). There was no significant difference between groups for the other parameters (Tampa Kinesiophobia Scale, Purdue Pegboard test, total active range movement, or handgrip strength: p > 0.05). CONCLUSION: This study shows that mirror therapy in postoperative rehabilitation of flexor tendon injuries is more effective than conventional in terms of reducing the severity of pain and restoring hand function.

Prospective external validation of an updated algorithm to quantify risk of febrile neutropenia in cancer patients after a cycle of chemotherapy.

PURPOSE: Febrile neutropenia resulting from chemotherapy is a significant cause of morbidity and mortality in cancer patients. We had previously published the associates of the risk of febrile neutropenia, and this study now extends and modifies the previous model as well as tests its external validity. METHODS: We have recruited documented febrile neutropenia cases with solid tumors, in addition to a selected control group of cancer patients from one institution treated between 2015 and 2019. We then united our sample with our previously published original derivation group, to modify and update our previous model by logistic regression analysis. Additionally, consecutive cancer patients from 5 institutions were recruited in 2020 to test external validity of the resultant algorithm. RESULTS: A total of 4075 cycles of chemotherapy in 1282 cases were recruited in the updated, new model derivation group, and a total of 8 variables were selected for the updated algorithm. In the new external validation group, 653 cycles of chemotherapy in 624 patients were analyzed, to indicate that after cycles without prophylactic granulocyte colony-stimulating factor (GCSF) usage, the algorithm yielded a sensitivity value of 91%, specificity of 40%, and an area under curve (AUC) figure of 0.78, when a risk cutoff threshold value of ≥ 0.20 is chosen. This algorithm is now embedded in a web application for free clinical use. CONCLUSION: Our algorithm identifies and quantifies the risk of febrile neutropenia in cancer patients. Further studies are required to improve this model with additional predictors.

Synthesis and molecular docking studies of some novel antimicrobial benzamides.

Common use of classical antibiotics has caused to the growing emergence of many resistant strains of pathogenic bacteria. Therefore, we aimed to synthesize a number of N-(2-hydroxy-(4 or 5)-nitrophenyl)benzamide derivatives as a new class of antimicrobial compounds. Moreover, our second goal is to predict the interaction between active structures and enzymes (DNA -gyrase and FtsA) in the binding mode. In this study, thirteen N-(2-hydroxy-(4 or 5-nitrophenyl)-substituted-benzamides were synthesized and determined for their antimicrobial activity using the microdilution method. According to this work, none of the compounds showed any activity against Candida albicans and its clinical isolate. Some of the benzamides (4N1, 5N1, 5N2) displayed very significant activity against Staphylococcus aureus and MSSA with <4 µg/ml MIC value, even they were found to be more potent than ceftazidime. 4N1 was also found to be more effective than gentamicin against Enterococcus faecalis clinical isolate. Molecular docking studies revealed that 4N1, 5N1, and 5N2 showed a good interactions with DNA-gyrase. Moreover, 5N1 has interacted with FtsA enzyme in the binding mode, as well. Only compound 5N4 displayed very good activity against Escherichia coli ATCC 25922. These findings showed us that 4N1, 5N1, 5N2, and 5N4 could be lead compounds to discover new antibacterial candidates against multidrug-resistant strains.

Molecular dynamics, thermodynamic, and mutational binding studies for tumor-specific LyP-1 in complex with p32.

Recent studies in tumor homing peptides have shown the specificity of LyP-1 (CGNKRTRGC) to tumor lymphatics. In this present work, we evaluated the possible interactions between cyclic LyP-1 and its receptor, p32, with molecular dynamics and docking studies in order to lead the design of novel LyP-1 derivatives, which could bind to p32 more effectively and perform enhanced antitumor effect. The total binding enthalpy energies have been obtained by MM-PBSA thermodynamic computations and the favorability of p32.LyP-1 complex in water has been shown by explicit water MD computations. The last 30 ns of molecular dynamics trajectory have shown the strong interaction of LyP-1 with the inner surface chains of p32, especially with chains B and C. ALA-SCAN mutagenesis studies have indicated the considerable influence of Asn3, Lys4, Arg5, and Arg7 amino acid residues on the specific binding of LyP-1. Within the knowledge of the critical role of p32 receptor in cancer cell metabolism, this study can lead to further developments in anticancer therapy by targeting p32 with LyP-1 derivatives as active targeting moiety. This data can also be applied for the development of new drug delivery systems in which LyP-1 can be used for its targeting and anticancer properties.

Characterisation of drug resistance of nosocomial ESBL-producing E. coli isolates obtained from a Turkish university hospital between 2009 and 2012 by pulsed field gel electrophoresis and antibiotic resistance tests.

In this study, drug resistance of 28 ESBL-producing Escherichia coli isolates obtained from 144 patients hospitalized at the Yüzüncüyil University Hospital at Van (YUH), Turkey, between 2009 and 2012 were characterized by pulsed field gel electrophoresis and antibiotic susceptibility tests. Antibiotic resistance profile was determined by Phoenix automated system (BD, USA). The ratio of ESBL-producing E. coli strains was determined to be 19.4% (28 out of 144 E. coli isolates). It was determined that the anaesthesiology, paediatrics and thoracic medicine intensive care units in YUH were cross-contaminated between 2009 and 2012 by ESBL-producing E. coli strains, which is a sign of nosocomial infection in YUH. Analysis of PFGE results gave rise to two main PFGE profiles, profile-A with four subprofiles and profile-B with three subprofiles, where profile-A predominates over profile-B (14%). Comparison of the antibiotic resistance profile with the PFGE profile yielded similarities while some differences also exist due to either identical restriction enzyme cutting sites with slightly different genetic sequences in between the cutting sites or newly formed restriction enzyme cutting sites that do not affect antibiotic resistance genes. Enterobacteriaceae, particularly E. coli, have developed resistance in YUH by producing ESBLs against oxyimino and non-oxyimino cephalosporins, and penicillin-type antibiotics. Therefore, more effective antibiotics such as cefoxitin or cefoperazone-sulbactam should be used for the treatment of future nosocomial infections in YUH while hospital staff should take care with hygiene, such as hand washing.

Effects of oxidative irrigants on root dentin structure: Attenuated Total Reflection Fourier Transform Infrared Spectroscopy study.

AIM: The aim of this study was to compare the effect of oxidative irrigants on the organic and inorganic structure of root canal dentin. METHODOLOGY: Fifty human 2nd premolar roots were used in the study. The dentin specimens prepared from those teeth were immersed in liquid nitrogen for 15 min. The frozen composition was titrated in a mixer and the obtained dentin powder was kept frozen at -70°C until use. Ten groups of 50mg dentin powder were immersed in agents (A: Ozone for 100 or 200 sec, B: 5.25% NaOCl, C: 2.25% NaOCl, D: 2% Chlorhexidine, E: 0.9% NaCl (control)) for 5 or 10 min. An Attenuated Total Reflection Fourier Transform Infrared Spectrophotometer (ATR FT-IR) was used to analyze dentin powder. The data were statistically analyzed by using Kruskall-Wallis analysis of variance. RESULTS: In all groups, collagen degradation was significantly increased compared to the control and 2% CHX groups (p<0.05). The use of ozone increased collagen degradation significantly compared to the use of 2.25% NaOCl and 2% Chlorhexidine for 5 min (p < 0.05). No significant differences were observed between ozone and 5.25% NaOCl-treated groups (p > 0.05). CONCLUSIONS: The structural composition of human dentin was significantly affected by the use of oxidative irrigants at higher concentrations.