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1.
PLoS One ; 19(2): e0297105, 2024.
Article in English | MEDLINE | ID: mdl-38358972

ABSTRACT

We present a Deep Learning approach to predict 3D folding structures of RNAs from their nucleic acid sequence. Our approach combines an autoregressive Deep Generative Model, Monte Carlo Tree Search, and a score model to find and rank the most likely folding structures for a given RNA sequence. We show that RNA de novo structure prediction by deep learning is possible at atom resolution, despite the low number of experimentally measured structures that can be used for training. We confirm the predictive power of our approach by achieving competitive results in a retrospective evaluation of the RNA-Puzzles prediction challenges, without using structural contact information from multiple sequence alignments or additional data from chemical probing experiments. Blind predictions for recent RNA-Puzzle challenges under the name "Dfold" further support the competitive performance of our approach.


Subject(s)
RNA , RNA/chemistry , Retrospective Studies , Sequence Alignment , Base Sequence
2.
Comput Biol Med ; 168: 107772, 2024 01.
Article in English | MEDLINE | ID: mdl-38064846

ABSTRACT

This study applies non-intrusive polynomial chaos expansion (NIPCE) surrogate modeling to analyze the performance of a rotary blood pump (RBP) across its operating range. We systematically investigate key parameters, including polynomial order, training data points, and data smoothness, while comparing them to test data. Using a polynomial order of 4 and a minimum of 20 training points, we successfully train a NIPCE model that accurately predicts pressure head and axial force within the specified operating point range ([0-5000] rpm and [0-7] l/min). We also assess the NIPCE model's ability to predict two-dimensional velocity data across the given range and find good overall agreement (mean absolute error = 0.1 m/s) with a test simulation under the same operating condition. Our approach extends current NIPCE modeling of RBPs by considering the entire operating range and providing validation guidelines. While acknowledging computational benefits, we emphasize the challenge of modeling discontinuous data and its relevance to clinically realistic operating points. We offer open access to our raw data and Python code, promoting reproducibility and accessibility within the scientific community. In conclusion, this study advances comprehensive NIPCE modeling of RBP performance and underlines how critically NIPCE parameters and rigorous validation affect results.


Subject(s)
Heart-Assist Devices , Reproducibility of Results , Computer Simulation , Models, Cardiovascular
3.
PeerJ ; 11: e15500, 2023.
Article in English | MEDLINE | ID: mdl-37361043

ABSTRACT

Understanding the mechanisms driving community assembly has been a major focus of ecological research for nearly a century, yet little is known about these mechanisms in commensal communities, particularly with respect to their historical/evolutionary components. Here, we use a large-scale dataset of 4,440 vascular plant species to explore the relationship between the evolutionary distinctiveness (ED) (as measured by the 'species evolutionary history' (SEH)) of host species and the phylogenetic diversity (PD) of their associated epiphyte species. Although there was considerable variation across hosts and their associated epiphyte species, they were largely unrelated to host SEH. Our results mostly support the idea that the determinants of epiphyte colonization success might involve host characteristics that are unrelated to host SEH (e.g., architectural differences between hosts). While determinants of PD of epiphyte assemblages are poorly known, they do not appear to be related to the evolutionary history of host species. Instead, they might be better explained by neutral processes of colonization and extinction. However, the high level of phylogenetic signal in epiphyte PD (independent of SEH) suggests it might still be influenced by yet unrecognized evolutionary determinants. This study highlights how little is still known about the phylogenetic determinants of epiphyte communities.


Subject(s)
Biological Evolution , Tracheophyta , Phylogeny , Symbiosis , Host Specificity
4.
Surg Innov ; 30(1): 126-129, 2023 Feb.
Article in English | MEDLINE | ID: mdl-35658779

ABSTRACT

Need: Bone resection using customized 3D-printed guides can improve accuracy, but the technique is still associated with clinically significant errors.Technical solution: We developed an inexpensive optical feedback system (OFS) that compares intraoperative 2D camera images to the pre-operative plan, and accurately depicts the surgeon's guide placement prior to cutting, reducing the errors in resection.Proof of concept: We simulated wide resections of a bone sarcoma on 24 cadaver femurs using 3 cutting guide types. Guide placement was measured using the OFS and compared to CT-scans showing the actual guide position. We carried out a second, controlled study on 20 sawbones, comparing the accuracy of the final bone cuts with and without the surgeon actively using the OFS to adjust the guide position before cutting.Results: For cadavers, in 2 of 3 planes, the position of the jig recorded by the OFS closely matched its actual position, with an accuracy of .87° ± .65°(r = .94) and 1.2° ± 1.3°(r = .81) in the transverse and sagittal planes, respectively. In the second study, OFS increased accuracy of the final cut about the transverse and sagittal planes, respectively by 53.1% (P = .011)/54.7% (P = .04) and 33% (P = .051)/38% (P = .042) in terms of rotation and translation.Next steps: Developing the OFS as a mobile application to reduce the processing time and improve accessibility in the operating room.Conclusion: The OFS could accurately depict the guide placement on the bone and significantly improve the surgical accuracy of 3D printed jigs.


Subject(s)
Bone Neoplasms , Surgery, Computer-Assisted , Humans , Surgery, Computer-Assisted/methods , Feedback , Bone Neoplasms/diagnostic imaging , Bone Neoplasms/surgery , Femur/diagnostic imaging , Femur/surgery
5.
Orthop Res Rev ; 14: 101-109, 2022.
Article in English | MEDLINE | ID: mdl-35422661

ABSTRACT

Introduction: Computer navigation and customized 3D-printed jigs improve accuracy during bone tumor resection, but such technologies can be bulky, costly, and require intraoperative radiation, or long lead time to be ready in OR. Methods: We developed a method utilizing a compact, inexpensive, non-X-ray based 3D surface light scanner to provide a visual aid that helps surgeons accurately draw osteotomy lines on the surface of exposed bone to reproduce a well-defined preoperative bone resection plan. We tested the accuracy of the method on 18 sawbones using a distal femur hemimetaphyseal resection model and compared it with a traditional, freehand method. Results: The method significantly reduces the positional error from 2.53 (±1.13) mm to 1.04 (±0.43) mm (p<0.001), and angular error of the front angle from 2.10° (±0.83°) to 0.80° (±0.66°) (p=0.001). The method also reduces the mean maximum deviation of the bone resection, with respect to the preoperative path, from 3.75mm to 2.69mm (p=0.003). However, no increased accuracy was observed at the back side of the bone surface where this method would not be expected to provide information. Discussion: In summary, we developed a novel 3D-LAD navigation technology. From the experimental study, we demonstrated that the method can improve the ability of surgeons to accurately draw the preoperative osteotomy lines and perform resection of a primary bone sarcoma, with comparison to traditional methods, using 18 sawbones.

6.
Environ Sci Pollut Res Int ; 29(29): 43501-43515, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35386087

ABSTRACT

Oil spills generate several environmental impacts and have become more common with the increase in petroleum extraction, refining, transportation, and trade. In soil, oil contamination increases water and nutrient availability and compaction, directly affecting plant growth and development. Different aspects of phytotoxicity can be observed and will vary according to the characteristics of soil and plants. Oil-contaminated soil also results in negative effects on biomass and changes in leaves and roots. Investigating the effects of oil contamination on plant growth and development can aid in the conservation of plant species and in the development of techniques such as bioremediation and biomonitoring. Thus, this review aims to discuss the main effects of oil contamination on plants, such as environmental stress and morphological, physiological, and anatomical changes, and the strategies developed by plants to survive contamination, as well as to identify plants with phytoremediation potential that can assist in removing oil from the environment.


Subject(s)
Petroleum Pollution , Petroleum , Soil Pollutants , Biodegradation, Environmental , Plant Roots/chemistry , Plants , Soil , Soil Pollutants/analysis
7.
Cardiovasc Eng Technol ; 13(4): 638-649, 2022 08.
Article in English | MEDLINE | ID: mdl-35031981

ABSTRACT

PURPOSE: Thrombosis ranks among the major complications in blood-carrying medical devices and a better understanding to influence the design related contribution to thrombosis is desirable. Over the past years many computational models of thrombosis have been developed. However, numerically cheap models able to predict localized thrombus risk in complex geometries are still lacking. The aim of the study was to develop and test a computationally efficient model for thrombus risk prediction in rotary blood pumps. METHODS: We used a two-stage approach to calculate thrombus risk. The first stage involves the computation of velocity and pressure fields by computational fluid dynamic simulations. At the second stage, platelet activation by mechanical and chemical stimuli was determined through species transport with an Eulerian approach. The model was compared with existing clinical data on thrombus deposition within the HeartMate II. Furthermore, an operating point and model parameter sensitivity analysis was performed. RESULTS: Our model shows good correlation (R2 > 0.93) with clinical data and identifies the bearing and outlet stator region of the HeartMate II as the location most prone to thrombus formation. The calculation of thrombus risk requires an additional 10-20 core hours of computation time. CONCLUSION: The concentration of activated platelets can be used as a surrogate and computationally low-cost marker to determine potential risk regions of thrombus deposition in a blood pump. Relative comparisons of thrombus risk are possible even considering the intrinsic uncertainty in model parameters and operating conditions.


Subject(s)
Heart-Assist Devices , Thrombosis , Blood Platelets , Heart-Assist Devices/adverse effects , Humans , Hydrodynamics , Platelet Activation , Thrombosis/etiology
8.
JCO Clin Cancer Inform ; 6: e2100126, 2022 01.
Article in English | MEDLINE | ID: mdl-35025669

ABSTRACT

PURPOSE: Intensive treatment protocols for aggressive hematologic malignancies harbor a high risk of serious clinical complications, such as infections. Current techniques of monitoring vital signs to detect such complications are cumbersome and often fail to diagnose them early. Continuous monitoring of vital signs and physical activity by means of an upper arm medical wearable allowing 24/7 streaming of such parameters may be a promising alternative. METHODS: This single-arm, single-center observational trial evaluated symptom-related patient-reported outcomes and feasibility of a wearable-based remote patient monitoring. All wearable data were reviewed retrospectively and were not available to the patient or clinical staff. A total of 79 patients (54 inpatients and 25 outpatients) participated and received standard-of-care treatment for a hematologic malignancy. In addition, the wearable was continuously worn and self-managed by the patient to record multiple parameters such as heart rate, oxygen saturation, and physical activity. RESULTS: Fifty-one patients (94.4%) in the inpatient cohort and 16 (64.0%) in the outpatient cohort reported gastrointestinal symptoms (diarrhea, nausea, and emesis), pain, dyspnea, or shivering in at least one visit. With the wearable, vital signs and physical activity were recorded for a total of 1,304.8 days. Recordings accounted for 78.0% (63.0-88.5; median [interquartile range]) of the potential recording time for the inpatient cohort and 84.6% (76.3-90.2) for the outpatient cohort. Adherence to the wearable was comparable in both cohorts, but decreased moderately over time during the trial. CONCLUSION: A high adherence to the wearable was observed in patients on intensive treatment protocols for a hematologic malignancy who experience high symptom burden. Remote patient monitoring of vital signs and physical activity was demonstrated to be feasible and of primarily sufficient quality.


Subject(s)
Hematologic Neoplasms , Wearable Electronic Devices , Feasibility Studies , Hematologic Neoplasms/diagnosis , Hematologic Neoplasms/therapy , Humans , Retrospective Studies , Vital Signs
9.
Invest Ophthalmol Vis Sci ; 63(1): 38, 2022 01 03.
Article in English | MEDLINE | ID: mdl-35084430

ABSTRACT

Purpose: Patients receiving chemotherapy may experience ocular discomfort and dry eye-like symptoms; the latter may be neuropathic in nature. This study assessed corneal and somatic hypersensitivity in male rats treated with paclitaxel and whether it was relieved by nicotinamide riboside (NR). Methods: Corneal sensitivity to tactile and chemical stimulation, basal tear production, and sensitivity of the hindpaw to tactile and cool stimuli were assessed before and after paclitaxel in the absence and presence of sustained treatment with 500 mg/kg per os NR. Corneal nerve density and hindpaw intraepidermal nerve fiber (IENF) density were also examined. Results: Paclitaxel-treated rats developed corneal hypersensitivity to tactile stimuli, enhanced sensitivity to capsaicin but not hyperosmolar saline, and increased basal tear production. Corneal nerve density visualized with anti-ß-tubulin or calcitonin gene-related peptide (CGRP) was unaffected. Paclitaxel induced tactile and cool hypersensitivity of the hindpaw and a loss of nonpeptidergic hindpaw IENFs visualized with anti-protein gene product (PGP) 9.5 and CGRP. NR reversed tactile hypersensitivity of the cornea without suppressing tear production or chemosensitivity; it did not alter corneal afferent density. NR also reversed tactile and cool hypersensitivity of the hindpaw without reversing the loss of hindpaw IENFs. Conclusions: These findings suggest that paclitaxel may be a good translational model for chemotherapy-induced ocular discomfort and that NR may be useful for its relief. The ability of NR to relieve somatic tactile hypersensitivity independent of changes in sensory nerve innervation suggests that reversal of terminal arbor degeneration is not critical to the actions of NR.


Subject(s)
Corneal Diseases/drug therapy , Hypersensitivity/drug therapy , Niacinamide/pharmacology , Paclitaxel/toxicity , Tears/metabolism , Animals , Corneal Diseases/chemically induced , Corneal Diseases/metabolism , Disease Models, Animal , Hypersensitivity/metabolism , Male , Rats , Rats, Sprague-Dawley , Vitamin B Complex/pharmacology
10.
J Surg Educ ; 79(1): 237-242, 2022.
Article in English | MEDLINE | ID: mdl-34538763

ABSTRACT

OBJECTIVE: The standard of care in treating congenital clubfoot is the Ponseti method. Resident education of this skill traditionally involves direct casting of patients with attending feedback. With increased clinical time demands, mastery of the skill may not be achievable using direct resident - patient interactions. We describe a novel Ponseti cast simulator using pressure sensors to teach this skill. DESIGN: A novel Ponseti cast simulator was constructed using a standardized model and pressure sensors. A pre-training baseline (trial 1) and post education (trial 2) was made and scored using an objective structured assessment of technical skill (OSATS) checklist. Pressure sensors were placed at the first metatarsal and talar head to record cast forces. SETTING: The study was performed in the Department of Orthopedic Surgery at an academic tertiary care hospital. PARTICIPANTS: Study participants included 6 junior orthopedic residents defined as post-graduate year (PGY) 1 to 3, 6 senior orthopedic residents (PGY 4,5), and a board -certified pediatric orthopedic surgeon to serve as a control. RESULTS: Trial 1 OSATS scores were significantly higher in senior residents (9.7 ± 1.5) than junior residents (5.2 ± 1.2) (p = 0.004). Trial 2 OSATS scores were also significantly higher in senior residents than junior residents: 13.7 ± 1.4 vs. 5.8 ± 1.6 (p = 0.003). Additionally, senior residents significantly improved scores between the first 2 trials 9.7 ± 1.5 vs. 13.7 ± 1.4 (p = 0.003), while junior residents did not 5.2 ± 1.2 vs. 5.8 ± 1.6 (p = 0.4566). In addition, there were no significant differences between junior, and senior resident Trial 1 talar head pressures or first metatarsal pressures, or Trial 2 first metatarsal pressures. CONCLUSIONS: This is the first casting simulation model to use pressure sensors as a way to objectively measure cast application pressure. This simulator may be useful in an orthopedic training programs to teach Ponseti casting.


Subject(s)
Clubfoot , Internship and Residency , Orthopedic Procedures , Orthopedics , Casts, Surgical , Child , Clinical Competence , Clubfoot/surgery , Computer Simulation , Humans , Orthopedic Procedures/methods , Orthopedics/education
11.
J Fungi (Basel) ; 7(7)2021 Jul 14.
Article in English | MEDLINE | ID: mdl-34356940

ABSTRACT

Extracellular vesicles (EVs) can transfer diverse RNA cargo for intercellular communication. EV-associated RNAs have been found in diverse fungi and were proposed to be relevant for pathogenesis in animal hosts. In plant-pathogen interactions, small RNAs are exchanged in a cross-kingdom RNAi warfare and EVs were considered to be a delivery mechanism. To extend the search for EV-associated molecules involved in plant-pathogen communication, we have characterised the repertoire of EV-associated mRNAs secreted by the maize smut pathogen, Ustilago maydis. For this initial survey, we examined EV-enriched fractions from axenic filamentous cultures that mimic infectious hyphae. EV-associated RNAs were resistant to degradation by RNases and the presence of intact mRNAs was evident. The set of mRNAs enriched inside EVs relative to the fungal cells are functionally distinct from those that are depleted from EVs. mRNAs encoding metabolic enzymes are particularly enriched. Intriguingly, mRNAs of some known effectors and other proteins linked to virulence were also found in EVs. Furthermore, several mRNAs enriched in EVs are also upregulated during infection, suggesting that EV-associated mRNAs may participate in plant-pathogen interactions.

12.
Arch Orthop Trauma Surg ; 141(12): 2155-2164, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34283279

ABSTRACT

INTRODUCTION: The impact of fulfillment of patient expectations throughout recovery on satisfaction in total knee arthroplasty (TKA) is not well understood. Utilizing a standardized TKA method with a robotically assisted (RA) platform, we investigated the impact of expectation fulfillment at 3-month (M) and 6-M on 1-year (Y) and 2-Y satisfaction. We hypothesize that early fulfillment of patient expectations is associated with improved midterm patient satisfaction. We also compare improvements in outcomes with RA-TKA to those of a recent large national TKA cohort study to determine whether RA-TKA meets or exceeds the current standard of care. MATERIALS AND METHODS: One hundred six patients were prospectively enrolled and underwent robotic-assisted TKA by a single surgeon using the OMNIBotics system. Patients completed KOOS and New Knee Society Score (KSS) preoperatively and at 3M, 6M, 1Y, and 2Y postoperatively. Expectation fulfillment was subdivided into patients who were below or above the average expectation score pre-operatively, or fulfillment of expectation score at 3M and 6M post TKA. The satisfaction of each group was then compared at 1Y and 2Y post TKA. Study cohort outcomes were compared to contemporary literature from the Function and Outcomes Research for Comparative Effectiveness in Total Joint Replacement (FORCE-TJR) database. RESULTS: Patients with greater than average KSS expectation fulfillment at 3M reported significantly higher KSS satisfaction scores at 1Y (34.9 ± 5.3 vs 30.6 ± 6.7, p = 0.0012), and patients with greater than average 6M expectation fulfillment reported improved satisfaction at 1Y (33.9 ± 5.9 vs 31.1 ± 6.7, p = 0.0330) and 2Y (35.2 ± 4.8 vs 32.4 ± 6.8, p = 0.0323). When compared to the FORCE-TJR database, no significant differences in post-operative KOOS outcomes were observed except for Sports and Recreation, for which the RAS group demonstrated higher scores (65.5 ± 30.0 vs 53.0 ± 27.1 p < 0.0001); however, the study cohort reported significantly greater improvements in KOOS Pain, Symptoms, Sports and Recreation, and Quality of Life at multiple time points up to 2 years post TKA. CONCLUSION: High early-expectation fulfillment was associated with improved satisfaction at 1Y and 2Y, indicating the importance of managing patient-specific post-operative care to ensure patients reach their pre-operative goals. Greater improvements in all KOOS sub-scores and in absolute Sports and Recreation at 1Y and 2Y were observed in this robotic-assisted cohort compared to a large contemporary database, indicating that RAS meets or exceeds current standard of care benchmarks for patient-reported outcomes.


Subject(s)
Arthroplasty, Replacement, Knee , Robotic Surgical Procedures , Cohort Studies , Humans , Motivation , Outcome Assessment, Health Care , Patient Satisfaction , Personal Satisfaction , Prospective Studies , Quality of Life
13.
Sensors (Basel) ; 20(23)2020 Dec 03.
Article in English | MEDLINE | ID: mdl-33287275

ABSTRACT

Knowledge of the propagation of sensor errors in strapdown inertial navigation is crucial for the design of inertial and integrated navigation systems. The propagation of initialization errors and deterministic sensor errors is well covered in the literature. If considered at all, the propagation of inertial sensor noise has typically been assessed for un-correlated (white) Gaussian noise. Real inertial sensor noise, however, is time-correlated (colored) and best described by a combination of different stochastic processes. In this paper, we demonstrate how a navigation system's response to colored noise input differs from the response to bias-like or white noise inputs. We present a method for assessing the navigation error from various inertial sensor noise processes without the need for time-consuming Monte Carlo simulations and demonstrate its application and validity with real sensor data. The proposed method is used to determine in which scenarios the sensor's real noise can be approximated by simple white Gaussian noise. The results indicate that neglecting colored sensor noise is justified for many applications, but should be checked individually for each sensor configuration and mission.

14.
West J Emerg Med ; 21(5): 1275-1282, 2020 Aug 20.
Article in English | MEDLINE | ID: mdl-32970586

ABSTRACT

INTRODUCTION: Few emergency department (ED)-specific fall-risk screening tools exist. The goals of this study were to externally validate Tiedemann et al's two-item, ED-specific fall screening tool and test handgrip strength to determine their ability to predict future falls. We hypothesized that both the two-item fall screening and handgrip strength would identify older adults at increased risk of falling. METHODS: A convenience sample of patients ages 65 and older presenting to a single-center academic ED were enrolled. Patients were asked screening questions and had their handgrip strength measured during their ED visit. Patients were given one point if they answered "yes" to "Are you taking six or more medications?" and two points for answering "yes" to "Have you had two or more falls in the past year?" to give a cumulative score from 0 to 3. Participants had monthly follow- ups, via postcard questionnaires, for six months after their ED visit. We performed sensitivity and specificity analyses, and used likelihood ratios and frequencies to assess the relationship between risk factors and falls, fall-related injury, and death. RESULTS: In this study, 247 participants were enrolled with 143 participants completing follow-up (58%). During the six-month follow-up period, 34% of participants had at least one fall and 30 patients died (12.1%). Fall rates for individual Tiedemann scores were 14.3%, 33.3%, 60.0% and 72.2% for scores of 0,1, 2 and 3, respectively. Low handgrip strength was associated with a higher proportion of falls (46.3%), but had poor sensitivity (52.1%). CONCLUSION: Handgrip strength was not sensitive in screening older adults for future falls. The Tiedemann rule differentiated older adults who were at high risk for future falls from low risk individuals, and can be considered by EDs wanting to screen older adults for future fall risk.


Subject(s)
Accidental Falls/prevention & control , Emergency Service, Hospital/organization & administration , Mass Screening , Risk Assessment/methods , Aged , Aged, 80 and over , Female , Hand Strength , Humans , Male , Mass Screening/methods , Mass Screening/standards , Predictive Value of Tests , Risk Factors , Surveys and Questionnaires
15.
Pain ; 161(10): 2364-2375, 2020 10.
Article in English | MEDLINE | ID: mdl-32433266

ABSTRACT

Nicotinamide riboside (NR) is a vitamin B3 precursor of NAD that blunts diabetic and chemotherapy-induced peripheral neuropathy in preclinical models. This study examined whether NR also blunts the loss of intraepidermal nerve fibers induced by paclitaxel, which is associated with peripheral neuropathy. The work was conducted in female rats with N-methyl-nitrosourea (MNU)-induced tumors of the mammary gland to increase its translational relevance, and to assess the interaction of NR with paclitaxel and NR's effect on tumor growth. Once daily oral administration of 200 mg/kg NR p.o. beginning with the first of 3 i.v. injections of 6.6 mg/kg paclitaxel to tumor-bearing rats significantly decreased paclitaxel-induced hypersensitivity to tactile and cool stimuli, as well as place-escape avoidance behaviors. It also blunted the loss of intraepidermal nerve fibers in tumor-bearing rats, as well as a separate cohort of tumor-naive rats. Unexpectedly, concomitant administration of NR during paclitaxel treatment further decreased tumor growth; thereafter, tumor growth resumed at the same rate as vehicle-treated controls. Administration of NR also decreased the percentage of Ki67-positive tumor cells in these rats. Once daily administration of NR did not seem to alter tumor growth or the percentage of Ki67-positive tumor cells in rats that were not treated with paclitaxel and followed for 3 months. These results further support the ability of NR to play a protective role after nerve injury. They also suggest that NR may not only alleviate peripheral neuropathy in patients receiving taxane chemotherapy, but also offer an added benefit by possibly enhancing its tumor-suppressing effects.


Subject(s)
Neoplasms , Paclitaxel/adverse effects , Paclitaxel/therapeutic use , Peripheral Nervous System Diseases , Animals , Female , Neoplasms/drug therapy , Niacinamide/analogs & derivatives , Peripheral Nervous System Diseases/chemically induced , Peripheral Nervous System Diseases/drug therapy , Pyridinium Compounds , Rats
16.
Bioinformatics ; 35(20): 3937-3943, 2019 10 15.
Article in English | MEDLINE | ID: mdl-30918943

ABSTRACT

MOTIVATION: Nucleic acids and proteins often have localized sequence motifs that enable highly specific interactions. Due to the biological relevance of sequence motifs, numerous inference methods have been developed. Recently, convolutional neural networks (CNNs) have achieved state of the art performance. These methods were able to learn transcription factor binding sites from ChIP-seq data, resulting in accurate predictions on test data. However, CNNs typically distribute learned motifs across multiple filters, making them difficult to interpret. Furthermore, networks trained on small datasets often do not generalize well to new sequences. RESULTS: Here we present circular filters, a novel convolutional architecture, that convolves sequences with circularly permutated variants of the same filter. We motivate circular filters by the observation that CNNs frequently learn filters that correspond to shifted and truncated variants of the true motif. Circular filters enable learning of full-length motifs and allow easy interpretation of the learned filters. We show that circular filters improve motif inference performance over a wide range of hyperparameters as well as sequence length. Furthermore, we show that CNNs with circular filters in most cases outperform conventional CNNs at inferring DNA binding sites from ChIP-seq data. AVAILABILITY AND IMPLEMENTATION: Code is available at https://github.com/christopherblum. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Neural Networks, Computer , Binding Sites , DNA , Protein Binding , Proteins
17.
Ecology ; 100(2): e02541, 2019 02.
Article in English | MEDLINE | ID: mdl-30707454

ABSTRACT

Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events.

18.
J Orthop Surg (Hong Kong) ; 26(2): 2309499018770925, 2018.
Article in English | MEDLINE | ID: mdl-29665764

ABSTRACT

BACKGROUND: Spontaneous osteonecrosis of the knee (SONK) is a poorly understood but debilitating disease entity. Total knee arthroplasty (TKA) is the standard of care for those patients who fail conservative management, but considering SONK's predilection for affecting a single knee compartment, unicompartmental knee arthroplasty (UKA) appears to be a more tailored option. Unfortunately, conflicting data exist on the utility of UKA in SONK. Thus, the purpose of this study was to evaluate functional outcomes and revision rates of UKA in the setting of SONK. METHODS: A systematic literature search was performed to evaluate all studies examining patients who underwent UKA for SONK. Screening of the articles was performed using multiple Boolean search strings, methodological index for non-randomized studies criteria, and other selected exclusion criteria. RESULTS: Seven studies were included, with a total of 276 knees (273 patients). The mean age was 68 years (64-74 years), with a mean body mass index of 26 kg/m2 (25-29 kg/m2). The final range of motion was 125° (124-126°). Standardized mean difference (SMD) of clinical improvement pre- and post-outcome was 3.39 ( p < 0.001). The improvement in the visual analog score was 57.03 points, with an SMD of 4.57 ( p < 0.001). Revision rates were determined to be 5.51% (95% confidence interval of 1.96-10.69%). CONCLUSION: Our meta-analysis demonstrated that in properly selected patients, UKA could be an excellent alternative to TKA for patients with SONK. These data show that UKA has few complications, significant improvements on functional outcomes, and good survivorship at a mean follow-up of 6 years.


Subject(s)
Arthroplasty, Replacement, Knee , Knee Joint , Osteonecrosis/surgery , Aged , Female , Humans , Male , Middle Aged , Treatment Outcome
19.
J Long Term Eff Med Implants ; 26(2): 167-171, 2016.
Article in English | MEDLINE | ID: mdl-28094741

ABSTRACT

Previous studies have examined multiple suture techniques for the repair of ruptured tendons. In this study, we investigated how the two- and four-stranded Krackow suture weave techniques compared with a novel Krackow/Bunnell suture technique. Our hypothesis was that the Krackow/Bunnell suture would have greater strength compared with the two- and four-stranded Krackow suture in terms of resistance to pullout from the muscle tendon. Thirty fresh bovine Achilles tendons were assigned randomly to three groups: (1) two-stranded Krackow, (2) fourstranded Krackow, and (3) the Krackow/Bunnell combination. After suture placement, all specimens were subjected to initial cyclic loading (0-200 N for 200 cycles) and then the tension to failure force defined as the pullout through the muscle tendon was evaluated. Significantly greater deformation before suture failure was seen in the Krackow/Bunnell group compared with the four-stranded Krackow construct (36.2 vs. 28.7 mm, p = 0.009), as well as greater energy required to rupture the suture (4635 vs. 3346 N/mm; p = 0.016). There was no significant difference with regard to the force to failure between the two groups (four-stranded Krackow vs. Krackow/Bunnell). The two-stranded Krackow was found to be inferior to both the four-stranded Krakow and the Krakow/Bunnell techniques with regard to load to failure. We have found that the Krackow/Bunnell suture technique is at least comparable to, if not superior to, the four-stranded Krackow technique with regard to deformation before suture failure and energy required to rupture the tendon. Therefore, the Krackow/Bunnell technique may be an optimal construct if the surgeon is concerned about suture pullout through the tendon; however, future studies evaluating this technique in the clinical setting are required before making any final conclusions for patient use.


Subject(s)
Suture Techniques , Tendons/surgery , Animals , Biomechanical Phenomena , Cattle , Random Allocation , Rupture , Sutures , Tensile Strength
20.
Environ Sci Pollut Res Int ; 22(9): 6968-88, 2015 May.
Article in English | MEDLINE | ID: mdl-25475620

ABSTRACT

Chemical leasing is a new and innovative approach of selling chemicals. It aims at reducing the risks emanating from hazardous substances and ensuring long-term economic success within a global system of producing and using chemicals. This paper explores how, through chemical leasing, the consumption of chemicals, energy, resources and the generation of related wastes can be reduced. It also analyses the substitution of hazardous chemicals as a tool to protect environmental, health and safety and hence ensure compliance with sustainability criteria. For this, we are proposing an evaluation methodology that seeks to provide an answer to the following research questions: (1) Does the application of chemical leasing promote sustainability in comparison to an existing chemicals production and management system? 2. If various chemical leasing project types are envisaged, which is the most promising in terms of sustainability? The proposed methodology includes a number of basic goals and sub-goals to assess the sustainability for eight different chemical leasing case studies that have been implemented both at the local and the national levels. The assessment is limited to the relative assessment of specific case studies and allows the comparisons of different projects in terms of their relative contribution to sustainable chemistry. The findings of our assessment demonstrate that chemical leasing can be regarded as promoting sustainable chemistry in five case studies with certainty. However, on the grounds of our assessment, we cannot conclude with certainty that chemical leasing has equivalent contribution to sustainable chemistry in respect of three further case studies.


Subject(s)
Chemistry/economics , Green Chemistry Technology , Hazardous Substances/economics , Industry , Leasing, Property , Commerce , Environmental Health
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