syedzayyan/paper_mill_benchmark huggingface dataset:
Physical energy-based ultrasound shifts M1 macrophage differentiation towards M2 state.

Recently, we read with interest the article entitled "unveiling the morphogenetic code: a new path at the intersection of physical energies and chemical signaling".In this paper, the investigation into the systematic and comprehensive bio-effects of physical energies prompted us to reflect on our research.We believe that ultrasound, which possesses a special physical energy, also has a certain positive regulatory effect on macrophages, and we have already obtained some preliminary research results that support our hypothesis.

Journal: World journal of stem cells (2022)
Publication types: Journal Article
Diagnosis of an actively bleeding brachial artery hematoma by contrast-enhanced ultrasound: A case report.

Active bleeding due to arterial injury following the acupuncture can sometimes represent a life-threatening complication.Only few reports of an actively bleeding hematoma diagnosed by contrast-enhanced ultrasound, which enables the depiction of vascular, have been reported.Case summary here, we report the case of a 75-year-old woman, who presented with sudden swelling, ecchymosis, and pain in the upper left limb.She underwent an acupuncture treatment of traditional chinese medicine followed by a deep shoulder massage 2 d before admission to hospital.A few hours after the massage, her left upper arm was red, swollen and progressively aggravated.Ultrasonography showed a large hematoma (11.2 cm × 3.5 cm × 3.4 cm) beside the left brachial artery.Color doppler ultrasound revealed that blood flow signals of the arteries branched into the hematoma.The contrast-enhanced ultrasound showed microbubbles from the brachial artery passing into the hematoma, diffused within the hematoma with the local surge of red blood cells, and disappearing after approximately 17 s.The microbubbles were likely due to bleeding from the arteries.After pressure bandaging treatment, the hematoma became smaller (3.1 cm × 1.7 cm) and organized according to ultrasonography performed 20 d later.Conclusion this case highlights the ultimate importance of contrast-enhanced ultrasound for the diagnosis of an actively bleeding hematoma.

Journal: World journal of clinical cases (2020)
Publication types: Case Reports;Journal Article
A scoping review of preprocessing methods for unstructured text data to assess data quality.

Introduction unstructured text data (utd) are increasingly found in many databases that were never intended to be used for research, including electronic medical record (emr) databases.Data quality can impact the usefulness of utd for research.Utd are typically prepared for analysis (i.e., preprocessed) and analyzed using natural language processing (nlp) techniques.Different nlp methods are used to preprocess utd and may affect data quality.Objective our objective was to systematically document current research and practices about nlp preprocessing methods to describe or improve the quality of utd, including utd found in emr databases.Methods a scoping review was undertaken of peer-reviewed studies published between december 2002 and january 2021.Scopus, web of science, pro quest, and ebscohost were searched for literature relevant to the study objective.Information extracted from the studies included article characteristics (i.e., year of publication, journal discipline), data characteristics, types of preprocessing methods, and data quality topics.Study data were presented using a narrative synthesis.Results a total of 41 articles were included in the scoping review; over 50% were published between 2016 and 2021.Almost 20% of the articles were published in health science journals.Common preprocessing methods included removal of extraneous text elements such as stop words, punctuation, and numbers, word tokenization, and parts of speech tagging.Data quality topics for articles about emr data included misspelled words, security (i.e., de-identification), word variability, sources of noise, quality of annotations, and ambiguity of abbreviations.Conclusions multiple nlp techniques have been proposed to preprocess utd, with some differences in techniques applied to emr data.There are similarities in the data quality dimensions used to characterize structured data and utd.While a few general-purpose measures of data quality that do not require external data; most of these focus on the measurement of noise.

Journal: International journal of population data science (2022)
Publication types: Review;Journal Article;Research Support, Non-U.S. Gov't
A comparison of distal femoral locking plates for distal femur fractures: Long working length versus short working length.

To compare long working length distal femoral locking plates with short working length for treating extra-articular distal femur fractures in terms of union and implant failure.Methods the randomised controlled trial was conducted at the lady reading hospital, peshawar, pakistan, from april 28, 2018, to march 10, 2021, and comprised all adult patients of either gender with extra-articular distal femur fractures who were randomised into two groups.Group a was exposed to long working length, while group b had short working length.Patients in both the groups were followed up regularly for one year for the assessment of fracture union and implant failure.Data was analysed using spss 22.Results in the group of the 61 patients, 30(49.2%) were in group a; 24(80%) males and 6(20%) females with overall mean age of 37.9±9.6 years.The remaining 31(50.8%) were in group b; 26(83.8%) males and 5(16.1%) females with overall mean age of 37.2±1 years.The mean working length in group a was 75±5mm and in group b it was 35±9mm.In group a 28(93.3%) fractures healed, while in group b 19(61.2%) fractures achieved union (p=0.01).Non-union was noted in 2(6.6%) patients in group a and 7(22.5%) in group b (p=0.08).Plate breakage was noted in 3(9.6%) patients and screw breakage in 2(6.4%) patients in group b and none in group a (p=0.0001).Conclusions long working length titanium locking plates were found to be better than short working length in achieving fracture union and avoiding implant failure.

Journal: JPMA. The Journal of the Pakistan Medical Association (2022)
Publication types: Randomized Controlled Trial;Journal Article
Bicentric validation of the navigated transcranial magnetic stimulation motor risk stratification model.

The authors sought to validate the navigated transcranial magnetic stimulation (n tms)-based risk stratification model.The postoperative motor outcome in glioma surgery may be preoperatively predicted based on data derived by n tms.The tumor-to-tract distance (ttd) and the interhemispheric resting motor threshold (rmt) ratio (as a surrogate parameter for cortical excitability) emerged as major factors related to a new postoperative deficit.Methods in this bicentric study, a consecutive prospectively collected cohort underwent n tms mapping with diffusion tensor imaging (dti) fiber tracking of the corticospinal tract prior to surgery of motor eloquent gliomas.The authors analyzed whether the following items were associated with the patient's outcome: patient characteristics, ttd, rmt value, and diffusivity parameters (fractional anisotropy [fa] and apparent diffusion coefficient [adc]).The authors assessed the validity of the published risk stratification model and derived a new model.Results a new postoperative motor deficit occurred in 36 of 165 patients (22%), of whom 20 patients still had a deficit after 3 months (13%; n3 months = 152).N tms-verified infiltration of the motor cortex as well as a ttd ≤ 8 mm were confirmed as risk factors.No new postoperative motor deficit occurred in patients with ttd > 8 mm.In contrast to the previous risk stratification, the rmt ratio was not substantially correlated with the motor outcome, but high rmt values of both the tumorous and healthy hemisphere were associated with worse motor outcome.The fa value was negatively associated with worsening of motor outcome.Accuracy analysis of the final model showed a high negative predictive value (npv), so the preoperative application may accurately predict the preservation of motor function in particular (day of discharge: sensitivity 47.2%, specificity 90.7%, positive predictive value [ppv] 58.6%, npv 86.0%; 3 months: sensitivity 85.0%, specificity 78.8%, ppv 37.8%, npv 97.2%).Conclusions this bicentric validation analysis further improved the model by adding the fa value of the corticospinal tract, demonstrating the relevance of n tms/n tms-based dti fiber tracking for clinical decision making.

Journal: Journal of neurosurgery (2022)
Publication types: Journal Article
Are selected IL-1 polymorphisms and selected subgingival microorganisms significantly associated to periodontitis in type 2 diabetes patients? a clinical study.

We evaluated the periodontal conditions in patients with type 2 diabetes mellitus compared to metabolically healthy controls, and determined whether periodontal interleukin genotypes and microorganisms differed between participants with and without type 2 diabetes mellitus.Methods from april 2011 to july 2012, we prospectively enrolled healthy controls and patients with type 2 diabetes mellitus.Evaluation included assessment of medical and periodontal findings.We also recorded the presence of several interleukin gene variants and specific microorganisms, both available through commercially available diagnostic kits.Statistical significance was tested by the chi-square test and student's t-test.Results we enrolled 52 patients with type 2 diabetes mellitus and 52 healthy controls.Compared with controls, periodontal disease was significantly more severe in patients with type 2 diabetes mellitus for the following: plaque index, bleeding on probing, pocket probing depth, clinical attachment loss, severe periodontal destruction (i.e., clinical attachment loss ≥ 5 mm), and number of teeth.However, statistical analysis failed to detect significant differences with respect to the periodontal-related interleukin genotypes (p ≥ 0.58) or the selected oral microbiota (p ≥ 0.15).Conclusion based on these results, it may be assumed that chronic periodontitis in patients with type 2 diabetes mellitus is most strongly associated with inadequate oral hygiene.Periodontal interleukin genotypes and differences in oral microbiota seem to play a subordinate role.

Journal: BMC oral health (2015)
Publication types: Journal Article
SUCCOR quality: validation of ESGO quality indicators for surgical treatment of cervical cancer.

To evaluate whether compliance with european society of gynaecological oncology (esgo) surgery quality indicators impacts disease-free survival in patients undergoing radical hysterectomy for cervical cancer.Methods in this retrospective cohort study, 15 esgo quality indicators were assessed in the succor database (patients who underwent radical hysterectomy for international federation of gynecology and obstetrics (figo) stage 2009 ib1, figo 2018 ib1, and ib2 cervical cancer between january 2013 and december 2014), and the final score ranged between 0 and 16 points.Centers with more than 13 points were classified as high-quality indicator compliance centers.We constructed a weighted cohort using inverse probability weighting to adjust for the variables.We compared disease-free survival and overall survival using cox proportional hazards regression analysis in the weighted cohort.Results a total of 838 patients were included in the study.The mean number of quality indicators compliance in this cohort was 13.6 (sd 1.45).A total of 479 (57.2%) patients were operated on at high compliance centers and 359 (42.8%) patients at low compliance centers.High compliance centers performed more open surgeries (58.4% vs 36.7%, p<0.01).Women who were operated on at centers with high compliance with quality indicators had a significantly lower risk of relapse (hr=0.39; 95% ci 0.25 to 0.61; p<0.001).The association was reduced, but remained significant, after further adjustment for conization, surgical approach, and use of manipulator surgery (hr=0.48; 95% ci 0.30 to 0.75; p=0.001) and adjustment for adjuvant therapy (hr=0.47; 95% ci 0.30 to 0.74; p=0.001).Risk of death from disease was significantly lower in women operated on at centers with high adherence to quality indicators (hr=0.43; 95% ci 0.19 to 0.97; p=0.041).However, the association was not significant after adjustment for conization, surgical approach, use of manipulator surgery, and adjuvant therapy.Conclusions patients with early cervical cancer who underwent radical hysterectomy in centers with high compliance with esgo quality indicators had a lower risk of recurrence and death.

Journal: International journal of gynecological cancer : official journal of the International Gynecological Cancer Society (2022)
Publication types: Journal Article
Single-nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana).

Premise progeny of avocado (persea americana) are highly variable due to high levels of heterozygosity.Breeding programs need molecular resources to allow the assessment of genetic differences and the selection of genotypes.Polymorphisms that uniquely identify different avocado cultivars provide a valuable tool to accelerate avocado research and development, including, for example, genotype selection.Methods a double-digest restriction site-associated dna sequencing (dd radseq) approach was used to screen 10 avocado cultivars for single-nucleotide polymorphisms (snps).The fragments were size selected with blue pippin and pcr using universal illumina primers, and catalog tags were then created with de novo alignment using stacks software.Catalog tags were tabulated and filtered to identify alleles unique to each cultivar.Results a total of 104 million sequences were collected, and 52 homozygous snps were identified that uniquely distinguished nine avocado cultivars.The cultivars carmen hass and hass have a strong genetic similarity and no homozygous snps distinguishing these cultivars could be identified; therefore, both cultivars were grouped together.Discussion the resource described here for cultivars of p.americanapresents a new and significant molecular resource that can enable targeted genotype selection, paternity analysis, germplasm genotyping, pollination dynamics investigation, and crop improvement.

Journal: Applications in plant sciences (2021)
Publication types: Journal Article
3D Object Detection Based on Attention and Multi-Scale Feature Fusion.

Three-dimensional object detection in the point cloud can provide more accurate object data for autonomous driving.In this paper, we propose a method named ma-mffc that uses an attention mechanism and a multi-scale feature fusion network with conv ne xt module to improve the accuracy of object detection.The multi-attention (ma) module contains point-channel attention and voxel attention, which are used in voxelization and 3d backbone.By considering the point-wise and channel-wise, the attention mechanism enhances the information of key points in voxels, suppresses background point clouds in voxelization, and improves the robustness of the network.The voxel attention module is used in the 3d backbone to obtain more robust and discriminative voxel features.The mffc module contains the multi-scale feature fusion network and the conv ne xt module; the multi-scale feature fusion network can extract rich feature information and improve the detection accuracy, and the convolutional layer is replaced with the conv ne xt module to enhance the feature extraction capability of the network.The experimental results show that the average accuracy is 64.60% for pedestrians and 80.92% for cyclists on the kitti dataset, which is 1.33% and 2.1% higher, respectively, compared with the baseline network, enabling more accurate detection and localization of more difficult objects.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Transmission of SARS-CoV-2 among children and staff in German daycare centres.

In daycare centres, the close contact of children with other children and employees favours the transmission of infections.The majority of children <6 years attend daycare programmes in germany, but the role of daycare centres in the sars-co v-2 pandemic is unclear.We investigated the transmission risk in daycare centres and the spread of sars-co v-2 to associated households.30 daycare groups with at least one recent laboratory-confirmed sars-co v-2 case were enrolled in the study (10/2020-06/2021).Close contact persons within daycare and households were examined over a 12-day period (repeated sars-co v-2 pcr tests, genetic sequencing of viruses, symptom diary).Households were interviewed to gain comprehensive information on each outbreak.We determined primary cases for all daycare groups.The number of secondary cases varied considerably between daycare groups.The pooled secondary attack rate (sar) across all 30 daycare centres was 9.6%.The sar tended to be higher when the alpha variant was detected (15.9%vs.5.1% with evidence of wild type).The household sar was 53.3%.Exposed daycare children were less likely to get infected with sars-co v-2 than employees (7.7%vs.15.5%).Containment measures in daycare programmes are critical to reduce sars-co v-2 transmission, especially to avoid spread to associated households.

Journal: Epidemiology and infection (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Immunoinformatic-based design of immune-boosting multiepitope subunit vaccines against monkeypox virus and validation through molecular dynamics and immune simulation.

Monkeypox virus is the causative agent of monkeypox disease, belonging to an orthopoxvirus genus, with a disease pattern similar to that of smallpox.The number of monkeypox cases have robustly increased recently in several countries around the world, potentially causing an international threat.Therefore, serious measures are indispensable to be taken to mitigate the spread of the disease and hence, under these circumstances, vaccination is the best choice to neutralize the monkeypox virus.In the current study, we used immunoinformatic approaches to target the l1r, b5r, and a33r proteins of the monkeypox virus to screen for immunogenic cytotoxic t-lymphocyte (ctl), helper t-lymphocyte (htl), and b-cell epitopes to construct multiepitope subunit vaccines.Various online tools predicted the best epitope from immunogenic targets (l1r, b5r, and a33r) of monkeypox virus.The predicted epitopes were joined together by different linkers and subjected to 3d structure prediction.Molecular dynamics simulation analysis confirmed the proper folding of the modeled proteins.The strong binding of the constructed vaccines with human tlr-2 was verified by the molecular docking and determination of dissociation constant values.The gc content and codon adaptation index (cai) values confirmed the high expression of the constructed vaccines in the p et-28a (+) expression vector.The immune response simulation data delineated that the injected vaccines robustly activated the immune system, triggering the production of high titers of ig g and ig m antibodies.In conclusion, this study provided a solid base of concept to develop dynamic and effective vaccines that contain several monkeypox virus-derived highly antigenic and nonallergenic peptides to control the current pandemic of monkeypox virus.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Modeling grating contrast discrimination dippers: The role of surround suppression.

We consider the role of nonlinear inhibition in physiologically realistic multineuronal models of v1 to predict the dipper functions from contrast discrimination experiments with sinusoidal gratings of different geometries.The dip in dipper functions has been attributed to an expansive transducer function, which itself is attributed to two nonlinear inhibitory mechanisms: contrast normalization and surround suppression.We ran five contrast discrimination experiments, with targets and masks of different sizes and configurations: small gabor target/small mask, small target/large mask, large target/large mask, small target/in-phase annular mask, and small target/out-of-phase annular mask.Our v1 modeling shows that the results for small gabor target/small mask, small target/large mask, large target/large mask configurations are easily explained only if the model includes surround suppression.This is compatible with the finding that an in-phase annular mask generates only little threshold elevation while the out-of-phase mask was more effective.Surrounding mask gratings cannot be equated with surround suppression at the receptive-field level.We examine whether normalization and surround suppression occur simultaneously (parallel model) or sequentially (a better reflection of neurophysiology).The akaike criterion difference showed that the sequential model was better than the parallel, but the difference was small.The large target/large mask dipper experiment was not well fit by our models, and we suggest that this may reflect selective attention for its uniquely larger test stimulus.The best-fit model replicates some behaviors of single v1 neurons, such as the decrease in receptive-field size with increasing contrast.

Journal: Journal of vision (2017)
Publication types: Journal Article
Beware of the DeBakey type I aortic dissection hidden by ischemic stroke: Two case reports.

De bakey type i aortic dissection is one of the rare etiologies of ischemic stroke.It is critical to identify arterial dissection before intravenous thrombolysis; otherwise, fatal hemorrhage may occur.Case summary in this report, we described 2 painless de bakey type i aortic dissection cases with initial symptoms similar to ischemic stroke.Sudden onset of conscious disturbance and limb weakness within minutes occurred in both cases.Hypotension was found in both cases.Thoracoabdominal computed tomography angiography was urgently performed due to unknown reason hypotension, and de bakey type i aortic dissection was confirmed.Intravenous thrombolysis was avoided because of timely diagnosis; however, they both eventually died of ruptured aortic dissection.Conclusion aortic dissection should always be excluded in ischemic stroke patients with unexplained hypotension or shock symptoms before intravenous thrombolytic therapy.

Journal: World journal of clinical cases (2022)
Publication types: Case Reports;Journal Article