Nevin Manimala

Protein J. 2021 Jun 27. doi: 10.1007/s10930-021-10011-y. Online ahead of print.

ABSTRACT

DNA-binding proteins play a vital role in cellular processes. It is an extremely urgent to develop a high-throughput method for efficiently identifying DNA-binding proteins. According to the current research situation, some methods in machine learning and deep learning show excellent computational speed and accuracy, which are worthy of application. In this work, a novel predictor was proposed to predict DNA binding proteins called UMAP-DBP. Firstly, the feature extraction of primary protein sequence was realized based on physicochemical distance transformation, Profile-based auto-cross covariance and General series correlation pseudo amino acid composition. Secondly, uniform manifold approximation and projection (UMAP) and feature importance score methods were used for feature selection; there is a progressive relationship between them. Finally, the Adaboost operation engine with jackknife test were adopted for predicting DNA-binding proteins. For the jackknife test on the BP1075 and BP594, we obtained an overall accuracy of 82.97% and 82.14%, Cohen’s kappa (CK) of 0.66 and 0.64, respectively. The results illustrate that a feasible method has been developed for predicting DNA-binding proteins by UMAP and Adaboost. This is the first study in which UMAP has been successfully applied to identify DNA-binding proteins. All the datasets and codes are accessible at https://github.com/Wang-Jinyue/UMAP-DBP .

PMID:34176069 | DOI:10.1007/s10930-021-10011-y

Radiol Med. 2021 Jun 26. doi: 10.1007/s11547-021-01386-0. Online ahead of print.

ABSTRACT

INTRODUCTION: Thyroid ultrasonography (US) is the first-step noninvasive and easily accessible diagnostic method widely used in the detection and characterization of nodular thyroid disease. We aimed to develop a TI-RADS, which is easy to apply and only relies on the counting of suspicious criteria. In order to measure the reliability of the system, we investigated its correlation with fine needle aspiration biopsy (FNAB) and post-surgery histological results.

MATERIALS AND METHODS: In this prospective study, 242 patients who had undergone FNAB with simultaneous cytopathologist in the radiology department between April and August 2016 were analyzed. Before FNAB, the thyroid gland was re-evaluated with US, and TI-RADS classification was made. Demographic characteristics, family thyroid cancer history and radiotherapy history to the neck region were noted.

RESULTS: Of the 242 patients, 17.3% were male (42 males/200 females). US-guided FNAB was applied to all patients. Mean age was 50 ± 13 years (min: 19, max: 82). Both FNAB and final post-surgery histology results showed that sex and age were not statistically significantly associated with malignancy (p = 0.193) TI-RADS criteria and FNAB results revealed a statistically significant association between irregular contours, the state of anteroposterior diameter being longer than transverse diameter, microcalcifications, marked hypoechogenicity, and malignancy (p < 0,05). Thirty patients were TI-RADS ≥ 4, 206 patients were TI-RADS ≤ 3 and there was a significant correlation between TI-RADS and Bethesda classification (p = 0.001). In addition, statistically significant associations were found between malignancy and family history of thyroid cancer (p = 0.035) and radiotherapy history to the neck region (p = 0.01).

CONCLUSION: TI-RADS system after nodule identification is based only on the counting of suspicious criteria. It will be safe and effective to recommend follow-up with low score TI-RADS, benign characters and insufficient FNAB results, and thus, unnecessary thyroidectomy operations will be prevented. It will be easier for surgeons to recommend surgery and persuade the patients for it when patients have high TI-RADS scores. TI-RADS has high power in detecting malignancy by recommending biopsy of suspicious nodules.

PMID:34176050 | DOI:10.1007/s11547-021-01386-0

Environ Sci Pollut Res Int. 2021 Jun 26. doi: 10.1007/s11356-021-15089-6. Online ahead of print.

ABSTRACT

Concentrations of eight trace elements (V, Cr, Ni, Cu, Zn, As, Cd, and Pb) were investigated in Posidonia oceanica leaf blades and sediments sampled from 23 stations along the Turkish-Mediterranean Sea coast. Trace element (TE) concentration in both sediment and P. oceanica showed a statistically significant distribution among sampling stations. Most of the TE concentration in samples varied remarkably among stations without a consistent trend. Concentrations of Zn, Cd, Cu, and Pb in the sediment of all of the sampling stations were determined as non-polluted based on the comparison with the sediment quality guideline index. More than a quarter of the sampling stations were found as moderately or heavily polluted for Cr, Ni, and As. The mean TE concentrations found in the sediment sample in the present study were similar to the concentrations reported from the different parts of the eastern Mediterranean Sea. TE concentrations in P. oceanica were generally lower compared to the concentrations in the sediment except for Cd, Zn, and Cu. While a positive correlation was found for Ni concentrations between sediment and P. oceanica samples, negative correlation was detected for V, Cr, Zn, Cu, As, and Cd concentrations between sediment and P. oceanica. The highest bioaccumulation factor in P. oceanica was calculated for Cd. The study area of the present study, especially the western sites (provinces of Antalya and Muğla), hosts millions of tourists annually and under the influence of intensive human activities in summer. Thus, coastal waters are heavily exposed to TEs and significantly positive correlations were detected between the anthropogenic TE pollutants (As, Cd, Cu, Zn, Pb, and V) and natural sourced TE (Ni and Cr). Based on our data, the Mediterranean Sea coast of Turkey does not present significant levels of Zd, Cd, Cu, and Pb pollution, whereas 65% of the stations were heavily polluted with As. Since As categorized as carcinogenic to humans, seafood sources should be monitored in terms of As concentrations. The current data might be useful in further TE-monitoring studies and TE discharge management strategies.

PMID:34176047 | DOI:10.1007/s11356-021-15089-6

Support Care Cancer. 2021 Jun 27. doi: 10.1007/s00520-021-06371-x. Online ahead of print.

ABSTRACT

BACKGROUND: Clinical guidelines recommend altering chemotherapy treatment by decreasing, delaying, or discontinuing dosing in patients who are experiencing chemotherapy-induced peripheral neuropathy. There are few data available on the clinical use of treatment alteration including the severity of CIPN at the time of treatment alteration.

METHODS: This was a retrospective analysis of patients receiving oxaliplatin on the NCCTG N08CB trial. Neuropathy severity was assessed at each cycle by clinicians and patients. Patients were classified as (1) completed treatment without alteration, (2) dose reduction or delay due to neuropathy, (3) discontinuation due to neuropathy, (4) discontinuation for other toxicity, or (5) discontinuation for another reason (5). Comparisons focused primarily on patients with alteration due to neuropathy (groups 2 and/or 3) compared with patients who completed treatment without alteration (group 1).

RESULTS: In 350 participants, 135 (39%) completed treatment without alteration, 70 (20%) had a dose reduction or delay due to neuropathy, and 35 (10%) discontinued early due to neuropathy. Clinician-assessed neuropathy severity was greater in patients at the time of dose reduction or delay compared with severity at the end of treatment in patients without alteration (p < 0.0001). Patient-reported neuropathy severity at cycle 4 was worse in patients who eventually had a reduction or delay as compared with patients who completed treatment without alteration (p = 0.017).

CONCLUSIONS: Treatment alterations due to neuropathy are common in patients receiving oxaliplatin for colon cancer and are associated with clinician-assessed neuropathy severity. Rapid increases in patient-reported neuropathy severity indicate a potential need for monitoring and intervention.

TRIAL REGISTRATION: Clinicaltrials.gov Identifier: NCT01099449 (NCCTG N08CB).

PMID:34176021 | DOI:10.1007/s00520-021-06371-x

Support Care Cancer. 2021 Jun 26. doi: 10.1007/s00520-021-06358-8. Online ahead of print.

ABSTRACT

BACKGROUND: A personalized risk model (PRM) that can categorize patients into high or low risk of ≥ grade 2 acute and/or delayed chemotherapy-induced nausea and vomiting (CINV) was previously developed. The current study assessed whether the PMR could accurately stratify patients’ risk for other commonly used CINV endpoints.

METHODS: Data was pooled from a previously reported trial evaluating CINV in patients with breast cancer (BC) receiving neo/adjuvant anthracycline-cyclophosphamide or carboplatin-based chemotherapy. The predictive ability of the PRM was compared to patient experience of any self-reported significant nausea, any vomiting, complete cycle response, and use of rescue medications, over all cycles of chemotherapy.

RESULTS: Data was available from 242 patients over 819 chemotherapy cycles. Irrespective of the chosen antiemetics, significant nausea was common when evaluated across repeated cycles of treatment with an overall incidence of 24.2% in low-risk patients and 34.6% in high-risk patients. Patients identified as high risk of CINV using the PRM were 4.73 (p = 0.011) times more likely to develop significant nausea than those identified as low risk. The PRM did not show any significant statistical differences between both groups in overall vomiting, complete cycle response, or rescue medications use.

CONCLUSION: The PRM was able to identify patients at greater risk of significant nausea but not the other CINV endpoints. As nausea remains a pertinent issue for patients with BC, the PRM could be used to identify these patients a priori for innovative treatment strategies.

PMID:34176018 | DOI:10.1007/s00520-021-06358-8

Int Ophthalmol. 2021 Jun 27. doi: 10.1007/s10792-021-01930-x. Online ahead of print.

ABSTRACT

PURPOSE: To analyze high and low contrast visual acuity and contrast sensitivity in diabetic patients without clinically significant macular edema associated or not with non-proliferative diabetic retinopathy.

METHODS: Cross-sectional study of 368 eyes of 368 patients classified into three groups: a) disease-free patients, b) patients with diabetes mellitus (DM) without diabetic retinopathy, c) DM patients with non-proliferative diabetic retinopathy. All patients underwent a complete ophthalmological examination that included high and low contrast visual acuity with 1.25%, 2.5% and 5% contrast chart and Pelli-Robson type contrast sensitivity test.

RESULTS: We observed no statistically significant differences regarding age, intraocular pressure, duration of diabetes or high contrast visual acuity. The eyes of patients with non-proliferative diabetic retinopathy had worse contrast sensitivity (p = 0.03, in both cases) and low contrast visual acuity at 1.5% (p = 0.03 and p = 0.01), 2.5% (p = 0.01, in both cases) and 5% (p = 0.02 and p = 0.04) than patients free of disease or without diabetic retinopathy.

CONCLUSIONS: Analysis of contrast sensitivity and low contrast visual acuity could be considered as markers of visual function impairment in the eyes of patients with non-proliferative diabetic retinopathy.

PMID:34176010 | DOI:10.1007/s10792-021-01930-x

Oral Radiol. 2021 Jun 26. doi: 10.1007/s11282-021-00549-z. Online ahead of print.

ABSTRACT

Specialists need to know how accurate and effective each radiographic procedure is, and which ones can provide better images for bone resorption around the apical periodontitis. Therefore, the researcher decided to conduct the present study with the aim of evaluate the accuracy values of cone-beam CT regarding apical periodontitis. The PubMed, Embase, ISI, Scopus, and Medicine have been used to search articles over the last 15 years between 2005 and December 2020. Meta-analysis data with 95% confidence interval (CI), Random effect model, and restricted maximum-likelihood methods were calculated. Random effects were used to deal with potential heterogeneity and I² showed heterogeneity. I² values above 50% signified moderate-to-high heterogeneity. The meta-analysis has been evaluated with the statistical software Stata/MP v.16 (The fastest version of Stata). One hundred and fifty-eight studies were selected to review the abstracts, six papers met these crucial criteria to do a systematic review and meta-analysis. Sensitivity and specificity of digital periapical radiography was 50% (ES 0.50; 95% CI 0.05, 0.95) and 83% (ES 0.83; 95% CI 0.52, 1.15), respectively. Sensitivity and specificity of cone-beam computed tomographic was 95% (ES 0.95; 95% CI 0.80, 1.00) and 90% (ES 0.90; 95% CI 0.78, 1.03), respectively. In conclusion, CBCT imaging reports values with excellent accuracy vs digital periapical radiography.

PMID:34176005 | DOI:10.1007/s11282-021-00549-z

Eur J Clin Microbiol Infect Dis. 2021 Jun 26. doi: 10.1007/s10096-021-04297-0. Online ahead of print.

ABSTRACT

In our tertiary care center, the reported susceptibility of E. coli blood isolates to amoxicillin/clavulanic acid exceeded 90% in 2005 and showed a progressive decrease to 50% by 2017. In this study, we investigate whether there is a real increase in resistant E. coli strains or if this apparent decline in reported susceptibility might be attributed to the substitution of CLSI by EUCAST guidelines in 2014. We randomly selected 237 E. coli blood isolates (stored at – 80 °C) from 1985 to 2018 and reassessed their MIC values, applying both the CLSI (fixed ratio of clavulanic acid) and EUCAST guidelines (fixed concentration of clavulanic acid). In parallel, the susceptibility of these isolates was retested by disk diffusion, according to the EUCAST guidelines. Whole genome sequencing was successfully performed on 233 of the 237 isolates. In only 130 of the 237 isolates (55.0%), testing according to the EUCAST and CLSI criteria delivered identical MIC values for amoxicillin/clavulanic acid. In 64 of the 237 isolates (27.0%), the MIC values diverged one dilution; in 38 (16.0%), two dilutions; and in five (2.1%), three dilutions. From these 107 discrepant results, testing according to EUCAST methodology revealed more resistant profiles in 93 E. coli strains (94.1%). Also, phenotypical susceptibility testing according to EUCAST guidelines tends to correlate better with the presence of beta-lactamase genes compared to CLSI testing procedure. This study highlights the low agreement between EUCAST and CLSI methodologies when performing MIC testing of amoxicillin/clavulanic acid. More strains are categorized as resistant when EUCAST guidelines are applied. The low agreement between EUCAST and CLSI was confirmed by WGS, since most of EUCAST resistant/CLSI sensitive isolates harbored beta-lactamase genes.

PMID:34175999 | DOI:10.1007/s10096-021-04297-0

Eur J Trauma Emerg Surg. 2021 Jun 26. doi: 10.1007/s00068-021-01739-4. Online ahead of print.

ABSTRACT

PURPOSE: Under-vehicle explosions caused by improvised explosive devices (IED) came to the public’s attention during armed conflicts. However, IEDs are also used by criminals in the civilian setting. This study aimed to determine the pattern of injury, medical management, and outcomes of civilians injured during under-vehicle explosions caused by IEDs.

METHODS: This is a retrospective cohort study based on the Israeli National Trauma Registry of patients injured from under vehicle explosions caused by IEDs during 2006-2020. Injuries resulting from terror attacks and war were excluded. Descriptive statistics were used for data analysis.

RESULTS: During the study period, 58 incidents were recorded, resulting in 74 patients who arrived alive to the hospitals and 17 who died on scene. Seventy-one (95.9%) were male with a median age of 32 years (IQR 24-42). 42% were severely injured (ISS ≥ 16). There was an average of 2.4 injured regions per patient, with extremity injuries being the most common (70.3%). Face (34%), abdomen (28%), and chest (22%) injuries were frequent. 45% were immediately transferred to the operating theatre, and 72% underwent at least one operation. Orthopedic surgeries were the most common interventions. 27 amputations were performed.

CONCLUSIONS: Injuries caused by under-vehicle IEDs in civilian settings differ from those caused by IEDs used during military conflicts or acts of terrorism: they are associated with fewer victims per incident, more severe injuries, more truncal injuries, and more lower extremity injuries requiring amputations. This can be attributed to the lack of personal and vehicle protection, and the different explosive types.

PMID:34175970 | DOI:10.1007/s00068-021-01739-4

Eur Arch Otorhinolaryngol. 2021 Jun 27. doi: 10.1007/s00405-021-06952-w. Online ahead of print.

ABSTRACT

PURPOSE: Bleeding during Functional endoscopic sinus surgery (FESS) can have adverse effect on surgical outcomes. This study evaluates if there is any benefit of adding epinephrine to the saline nasal irrigation in patients undergoing elective FESS for chronic rhinosinusitis.

METHODS: A prospective, randomized, double-blinded study was performed. Fifty ASA I or II patients undergoing FESS were randomized to have irrigation either with normal saline or (1:100,000) epinephrine in normal saline during surgery. Outcomes measure included the Boezaart grading scale to assess the intraoperative surgical field, surgeon’s satisfaction with field visualization and bleeding which was evaluated in a 10 cm visual analog scale, estimated blood loss as well as hemodynamic parameters changes.

RESULTS: There was no statistically significant difference in the studied variables between both groups. However in patients with higher than 12 Lund-Mackay score the volume of blood loss was significantly less in the epinephrine group. All surgical procedures were completed and there were no operative complications or any reported perioperative cardiovascular events.

CONCLUSIONS: Intraoperative irrigation with saline-epinephrine solution at a concentration of (1:100,000) is safe and does not change heart rate or blood pressure but is unlikely to improve the setting of intraoperative surgical field except for decreasing the volume of blood loss in patients with high Lund-Mackay score.

PMID:34175968 | DOI:10.1007/s00405-021-06952-w