bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic contouring system for cervical cancer using convolutional neural networks
Authors: Rhee Dong Joo , Jhingran Anuja , Rigaud Bastien , Netherton Tucker , Cardenas Carlos E. , Zhang Lifei , Vedam Sastry , Kry Stephen , Brock Kristy K. , Shaw William , O’Reilly Frederika , Parkes Jeannette , Burger Hester , Fakie Nazia , Trauernicht Chris , Simonds Hannah , Court Laurence E. 
Published: September 2020

PurposeTo develop a tool for the automatic contouring of clinical treatment volumes (CTVs) and normal tissues for radiotherapy treatment planning in cervical cancer patients.MethodsAn auto‐contouring tool based on convolutional neural networks (CNN) was developed to delineate three cervical CTVs and 11 normal structures (seven OARs, four bony structures) in cervical cancer treatment for use with the Radiation Planning Assistant, a web‐based automatic plan generation system. A total of 2254 retrospective clinical computed tomography (CT) scans from a single cancer center and 210 CT scans from a segmentation challenge were used to train and validate the CNN‐based auto‐contouring tool. The accuracy of the tool was evaluated by calculating the Sørensen‐dice similarity coefficient (DSC) and mean surface and Hausdorff distances between the automatically generated contours and physician‐drawn contours on 140 internal CT scans. A radiation oncologist scored the automatically generated contours on 30 external CT scans from three South African hospitals.ResultsThe average DSC, mean surface distance, and Hausdorff distance of our CNN‐based tool were 0.86/0.19 cm/2.02 cm for the primary CTV, 0.81/0.21 cm/2.09 cm for the nodal CTV, 0.76/0.27 cm/2.00 cm for the PAN CTV, 0.89/0.11 cm/1.07 cm for the bladder, 0.81/0.18 cm/1.66 cm for the rectum, 0.90/0.06 cm/0.65 cm for the spinal cord, 0.94/0.06 cm/0.60 cm for the left femur, 0.93/0.07 cm/0.66 cm for the right femur, 0.94/0.08 cm/0.76 cm for the left kidney, 0.95/0.07 cm/0.84 cm for the right kidney, 0.93/0.05 cm/1.06 cm for the pelvic bone, 0.91/0.07 cm/1.25 cm for the sacrum, 0.91/0.07 cm/0.53 cm for the L4 vertebral body, and 0.90/0.08 cm/0.68 cm for the L5 vertebral bodies. On average, 80% of the CTVs, 97% of the organ at risk, and 98% of the bony structure contours in the external test dataset were clinically acceptable based on physician review.ConclusionsOur CNN‐based auto‐contouring tool performed well on both internal and external datasets and had a high rate of clinical acceptability.
Determination of the absorbed dose to water for medium‐energy x‐ray beams using Fricke dosimetry
Authors: Rosado Paulo Henrique , Salata Camila , David Mariano Gazineu , Mantuano Andrea , Pickler Arissa , Mota Carla Lemos , de Almeida Carlos E. 
Published: September 2020

PurposeFor x‐ray beams in the low and medium energy range, reference dosimetry is established in terms of air kerma. Fricke dosimetry has shown great potential in the absolute measurements of the absorbed dose to water for high‐energy ranges. Therefore, the main purpose of this work was to compare the absorbed dose to water for medium‐energy x‐ray beams obtained through Fricke dosimetry with that obtained from the air kerma rate.MethodsTo determine the absorbed dose to water using Fricke dosimetry, the polyethylene bags methodology was chosen. Fricke solution was irradiated at four different beam qualities. The absorbed dose to water values obtained using Fricke dosimetry were compared to those obtained using the standard protocol, using the Z‐score.ResultsValues of the Z‐score were <2 for all measurements of absorbed dose to water, which means that the values obtained using Fricke dosimetry are equivalent to those obtained using the reference protocol. The combined standard uncertainty for the absorbed dose to water obtained by Fricke dosimetry was lower than that obtained with the ionization chamber.ConclusionsChemical dosimetry using a standard FeSO4 solution has been demonstrated to be a potential option as a standard for the quantity absorbed dose to water for medium kV x‐ray qualities.
Technical Note: Scintillation markers for real‐time visual source tracking during skin high dose rate brachytherapy
Authors: Huynh Elizabeth , Bhagwat Mandar S. 
Published: September 2020

BackgroundTreatment misadministration during high dose rate (HDR) brachytherapy is mainly caused due to gross errors in incorrect manual entry of catheter length and manual connection of hardware. The probability of these errors increases with increasing complexity of a surface applicator. A simple, real‐time visual verification method was developed using a scintillator to enhance quality assurance (QA) measures for HDR surface brachytherapy and thus reduce manual errors and improve patient safety.Materials and methodsScintillation markers were fabricated from cerium‐doped lutetium yttrium orthosilicate (LYSO) embedded in a polymer compound to form 5‐mm diameter markers. To verify catheter‐transfer tube connections, markers were attached to each channel of a Freiburg flap and irradiated with an 192Ir source. To determine if the source reached the edge of a target, markers were placed along the periphery. The HDR source was visually tracked by following the illumination from the markers. The response of the markers was also verified in the presence of thermoplastic material overlaid on the Freiburg applicator.ResultsScintillation markers emitted intense blue visible light upon irradiation when the HDR source was beneath the marker, verifying the source’s presence in the correct catheter. The signal was clearly visible even when the marker was placed on top of the thermoplastic material covering the Freiburg Flap. Crosstalk from adjacent catheters was <50% of the maximum light intensity.ConclusionScintillation markers and paint were developed to successfully meet the challenge of visually tracking of HDR source during brachytherapy by surface applicators. This direct visualization of source allows real‐time catheter verification during treatment, and correct superficial target coverage, thus preventing a medical event. It can easily be integrated into pre‐existing QA program.
Calibrationless parallel imaging reconstruction for multislice MR data using low‐rank tensor completion
Authors: Liu Yilong , Yi Zheyuan , Zhao Yujiao , Chen Fei , Feng Yanqiu , Guo Hua , Leong Alex T. L. , Wu Ed X. 
Published: September 2020

PurposeTo provide joint calibrationless parallel imaging reconstruction of highly accelerated multislice 2D MR k‐space data.MethodsAdjacent image slices in multislice MR data have similar coil sensitivity maps, spatial support, and image content. Such similarities can be utilized to improve image quality by reconstructing multiple slices jointly with low‐rank tensor completion. Specifically, the multichannel k‐space data from multiple slices are constructed into a block‐wise Hankel tensor and iteratively updated by promoting tensor low‐rankness through higher‐order SVD. This multislice block‐wise Hankel tensor completion was implemented for 2D spiral and Cartesian k‐space undersampling where sampling patterns vary between adjacent slices. The approach was evaluated with human brain MR data and compared to the traditional single‐slice simultaneous autocalibrating and k‐space estimation reconstruction.ResultsThe proposed multislice block‐wise Hankel tensor completion approach robustly reconstructed highly undersampled multislice 2D spiral and Cartesian data. It produced substantially lower level of artifacts compared to the traditional single‐slice simultaneous autocalibrating and k‐space estimation reconstruction. Quantitative evaluation using error maps and root mean square error demonstrated its significantly improved performance in terms of residual artifacts and root mean square error.ConclusionOur proposed multislice block‐wise Hankel tensor completion method exploits the similar coil sensitivity and image content within multislice MR data through a tensor completion framework. It offers a new and effective approach to acquire and reconstruct highly undersampled multislice MR data in a calibrationless manner.
Chronic inflammatory demyelinating polyradiculoneuropathy—Diagnostic pitfalls and treatment approach
Authors: Stino Amro M. , Naddaf Elie , Dyck Peter J. , Dyck P. James B. 
Published: September 2020

AbstractChronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is characterized by progressive weakness and sensory loss, often affecting patientsʼ ability to walk and perform activities of daily living independently. With the lack of a diagnostic biomarker, the diagnosis relies on clinical suspicion, clinical findings, and the demonstration of demyelinating changes on electrodiagnostic (EDx) testing and nerve pathology. As a result, patients can often be misdiagnosed with CIDP and unnecessarily treated with immunotherapy. Interpreting the EDx testing and cerebrospinal fluid findings in light of the clinical phenotype, recognizing atypical forms of CIDP, and screening for CIDP mimickers are the mainstays of the approach to patients suspected of having CIDP, and are detailed in this review. We also review the currently available treatment options, including intravenous immunoglobulin (IVIg), corticosteroids (CCS), and plasma exchange (PE), and discuss how to approach treatment‐refractory cases. Finally, we emphasize the need to adopt objective outcome measures to monitor treatment response.
Overexpression of ArabidopsismicroRNA167 induces salicylic acid‐dependent defense against Pseudomonas syringae through the regulation of its targets ARF6 and ARF8
Authors: Caruana Julie C. , Dhar Nikhilesh , Raina Ramesh 
Published: September 2020

AbstractmicroRNAs are powerful regulators of growth, development, and stress responses in plants. The Arabidopsis thaliana microRNA miR167 was previously found to regulate diverse processes including flower development, root development, and response to osmotic stress by controlling the patterns of expression of its target genes AUXIN RESPONSE FACTOR 6 (ARF6), ARF8, and IAA‐Ala RESISTANT 3. Here, we report that miR167 also modulates defense against pathogens through ARF6 and ARF8. miR167 is differentially expressed in response to the bacterial pathogen Pseudomonas syringae, and overexpression of miR167 confers very high levels of resistance. This resistance appears to be due to suppression of auxin responses and is partially dependent upon salicylic acid signaling, and also depends upon altered stomatal behavior in these plants. Closure of stomata upon the detection of P. syringae is an important aspect of the basal defense response, as it prevents bacterial cells from entering the leaf interior and causing infection. Plants overexpressing miR167 constitutively maintain small stomatal apertures, resulting in very high resistance when the pathogen is inoculated onto the leaf surface. Additionally, the systemic acquired resistance (SAR) response is severely compromised in plants overexpressing miR167, in agreement with previous work showing that the activation of SAR requires intact auxin signaling responses. This work highlights a new role for miR167, and also emphasizes the importance of hormonal balance in short‐ and long‐term defense and of stomata as an initial barrier to pathogen entry.
Optimization of UAS‐based high‐throughput phenotyping to estimate plant health and grain yield in sorghum
Authors: Galli Giovanni , Horne David W. , Collins S. Delroy , Jung Jinha , Chang Anjin , Fritsche‐Neto Roberto , Rooney William L. 
Published: September 2020

AbstractHigh‐throughput phenotyping (HTP) has enabled the acquisition of vast amounts of data. Therefore, finding the most informative phenological stage(s) and high‐throughput traits could lead to significant optimization of HTP‐assisted selection. An investigation as to when phenotypic data should be collected and how it should be processed from unmanned aerial system (UAS) imagery for the optimization and assessment of two primary traits in grain sorghum [Sorghum bicolor (L). Moench], namely, grain yield and plant health (based on anthracnose scores) was conducted. By evaluating multiple flight dates across the growing season via multispectral UAS‐based imagery, a set of scenarios composed of combinations of flight dates and vegetation indices were constructed for analysis. In this sense, results showed no increase in predictive ability when combining multiple vegetation indices. Hence, using only an index with a higher predictive ability (e.g., normalized difference vegetation index (NDVI) or modified simple ratio (MSR) for plant health with 0.75; and any tested index but chlorophyll index (CIg) for grain yield with ∼0.55) is recommended. Likewise, the combining of multiple flights did not result in a significant increase in predictive ability for either primary trait. Thus, we observed that a single flight for each trait (e.g., 121 d after sowing with 0.81 for plant health; 104 d after sowing with 0.59 for grain yield) was optimal. Concerning, the predictive algorithms examined, partial least squares regression (PLSR) and neural network, results were similar, with PLSR generally outperforming. In addition, we discuss our findings from an application standpoint of a field‐based breeding program and suggest additional optimization options.
Iris: Interactive all‐in‐one graphical validation of 3D protein model iterations
Authors: Rochira William , Agirre Jon 
Published: September 2020

AbstractIris validation is a Python package created to represent comprehensive per‐residue validation metrics for entire protein chains in a compact, readable and interactive view. These metrics can either be calculated by Iris, or by a third‐party program such as MolProbity. We show that those parts of a protein model requiring attention may generate ripples across the metrics on the diagram, immediately catching the modeler's attention. Iris can run as a standalone tool, or be plugged into existing structural biology software to display per‐chain model quality at a glance, with a particular emphasis on evaluating incremental changes resulting from the iterative nature of model building and refinement. Finally, the integration of Iris into the CCP4i2 graphical user interface is provided as a showcase of its pluggable design.
Effect of Eriocalyxin B on prostatic inflammation and pelvic pain in a mouse model of experimental autoimmune prostatitis
Authors: Zhang Li‐Gang , Yu Zi‐Qiang , Yang Cheng , Chen Jing , Zhan Chang‐Sheng , Chen Xian‐Guo , Zhang Li , Hao Zong‐Yao , Liang Chao‐Zhao 
Published: September 2020

AbstractBackgroundChronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a common disease in males. Eriocalyxin B (EriB), a natural diterpenoid purified from Isodon eriocalyx var. laxiflora, was previously reported to have antitumor effects via multiple immune‐related pathways. In this study, we investigated the effect of EriB on CP/CPPS using a mouse model of experimental autoimmune prostatitis (EAP) and explored its potential mechanisms.MethodsThe EAP model was established in nonobese diabetic mice by intradermal injecting a mixture of prostate antigens and Complete Freund's Adjuvant on days 0 and 28. Then, EAP mice received daily intraperitoneal injections of EriB (5 or 10 mg/kg/d) for 14 days, from days 28 to 42 (EAP+EriB5 or EAP+EriB10 groups). The histopathological appearance of the prostate tissues was evaluated. Chronic pelvic pain development was assessed by cutaneous allodynia. Inflammatory cytokines were measured by enzyme‐linked immunosorbent assay tests. We then explored anti‐inflammatory potential mechanisms of EriB by studying the effects of PI3K inhibitor wortmannin (EAP+EriB10+Wort group) and NF‐κB inhibitor SC75741 (EAP+EriB10+SC group) on prostate inflammation and pelvic pain using this model.ResultsHistological analyses revealed significant prostate inflammation in EAP mice compared with control mice. Significantly increased pelvic pain was detected in EAP mice (P < .05). Compared with the EAP+Veh group, chronic pain development, histological appearance, and cytokine levels demonstrated that EriB could alleviate the severity of EAP in a dose‐dependent manner though upregulation of the PI3K/Akt/mTOR pathway and downregulation of the NF‐κB pathway. Further mechanism research demonstrated that the PI3K/AKT/mTOR pathway could be blocked by wortmannin, but was not affected by SC75741. In addition, the NF‐κB pathway could be further inhibited by SC75741 compared with the EAP+EriB10+Veh group. However, wortmannin could reactivate the NF‐κB pathway, indicating that the PI3K/AKT/mTOR pathway negatively regulates the NF‐κB pathway during EriB treatment.ConclusionsThe results of the present study suggested that EriB could alleviate the severity of prostatic inflammation and pelvic pain in an EAP mouse model. These findings may broaden the value of EriB as a promising candidate for the treatment of CP/CPPS.
Antiallodynic effect of PhAR‐DBH‐Me involves cannabinoid and TRPV1 receptors
Authors: Quiñonez‐Bastidas Geovanna Nallely , Palomino‐Hernández Oscar , López‐Ortíz Manuel , Rocha‐González Héctor Isaac , González‐Anduaga Gloria Melisa , Regla Ignacio , Navarrete Andrés 
Published: September 2020

AbstractThe antiallodynic effect of PhAR‐DBH‐Me was evaluated on two models of neuropathic pain, and the potential roles of CB1, CB2, and TRPV1 receptors as molecular targets of PhAR‐DBH‐Me were studied. Female Wistar rats were submitted to L5/L6 spinal nerve ligation (SNL) or repeated doses of cisplatin (0.1 mg/kg, i.p.) to induce experimental neuropathy. Then, tactile allodynia was determined, and animals were treated with logarithmic doses of PhAR‐DBH‐Me (3.2‐100 mg/kg, i.p.). To evaluate the mechanism of action of PhAR‐DBH‐Me, in silico studies using crystallized structures of CB1, CB2, and TRPV1 receptors were performed. To corroborate the computational insights, animals were intraperitoneally administrated with antagonists for CB1 (AM‐251, 3 mg/kg), CB2 (AM‐630, 1 mg/kg), and TRPV1 receptors (capsazepine, 3 mg/kg), 15 min before to PhAR‐DBH‐Me (100 mg/kg) administration. Vagal stimulation evoked on striated muscle contraction in esophagus, was used to elicited pharmacological response of PhAR‐DBH‐ME on nervous tissue. Systemic administration of PhAR‐DBH‐Me reduced the SNL‐ and cisplatin‐induced allodynia. Docking studies suggested that PhAR‐DBH‐Me acts as an agonist for CB1, CB2, and TRPV1 receptors, with similar affinity to the endogenous ligand anandamide. Moreover antiallodynic effect of PhAR‐DBH‐Me was partially prevented by administration of AM‐251 and AM‐630, and completely prevented by capsazepine. Finally, PhAR‐DBH‐Me decreased the vagally evoked electrical response in esophagus rat. Taken together, results indicate that PhAR‐DBH‐Me induces an antiallodynic effect through partial activation of CB1 and CB2 receptors, as well as desensitization of TRPV1 receptors. Data also shed light on the novel vanilloid nature of the synthetic compound PhAR‐DBH‐Me.
A dicamba resistance‐endowing IAA16 mutation leads to significant vegetative growth defects and impaired competitiveness in kochia (Bassia scoparia)†
Authors: Wu Chenxi , LeClere Sherry , Liu Kang , Paciorek Marta , Perez‐Jones Alejandro , Westra Phil , Sammons R Douglas 
Published: September 2020

AbstractBACKGROUNDPrecise quantification of the fitness cost of synthetic auxin resistance has been impeded by lack of knowledge about the genetic basis of resistance in weeds. Recent elucidation of a resistance‐endowing IAA16 mutation (G73N) in the key weed species kochia (Bassia scoparia), allows detailed characterization of the contribution of resistance alleles to weed fitness, both in the presence and absence of herbicides. Different G73N genotypes from a segregating resistant parental line (9425) were characterized for cross‐resistance to dicamba, 2,4‐d and fluroxypyr, and changes on stem/leaf morphology and plant architecture. Plant competitiveness and dominance of the fitness effects was quantified through measuring biomass and seed production of three F2 lines in two runs of glasshouse replacement series studies.RESULTSG73N confers robust resistance to dicamba but only moderate to weak resistance to 2,4‐D and fluroxypyr. G73N mutant plants displayed significant vegetative growth defects: (i) they were 30–50% shorter, with a more tumbling style plant architecture, and (ii) they had thicker and more ovate (versus lanceolate and linear) leaf blades with lower photosynthesis efficiency, and 40–60% smaller stems with less‐developed vascular bundle systems. F2 mutant plants had impaired plant competitiveness, which can lead to 80‐90% less biomass and seed production in the replacement series study. The pleiotropic effects of G73N were mostly semidominant (0.5) and fluctuated with the environments and traits measured.CONCLUSIONG73N is associated with significant vegetative growth defects and reduced competitiveness in synthetic auxin‐resistant kochia. Management practices should target resistant kochia's high vulnerability to competition in order to effectively contain the spread of resistance.
Monitoring multivariate coefficient of variation with upward Shewhart and EWMA charts in the presence of measurement errors using the linear covariate error model
Authors: Ayyoub Heba N. , Khoo Michael B. C. , Lee Ming Ha , Haq Abdul 
Published: September 2020

AbstractIn practice, measurement errors exist and ignoring their presence may lead to erroneous conclusions in the actual performance of control charts. The implementation of the existing multivariate coefficient of variation (MCV) charts ignores the presence of measurement errors. To address this concern, the performances of the upward Shewhart‐MCV and exponentially weighted moving average MCV charts for detecting increasing MCV shifts, using a linear covariate error model, are investigated. Explicit mathematical expressions are derived to compute the limits and average run lengths of the charts in the presence of measurement errors. Finally, an illustrative example using a real‐life dataset is presented to demonstrate the charts’ implementation.
Application of β‐Nitrostyrene in Multicomponent Reactions for the Synthesis of Pyrrole Derivatives
Authors: Rostami Hedieh , Shiri Lotfi 
Published: September 2020

Abstractβ‐nitrostyrene is an important and effective starting material for the synthesis of heterocycle compounds such as pyrrole derivatives via multicomponent reactions. β‐nitrostyrene in its reactions undergoes Michael addition. Pyrroles derivatives are an important group of heterocycle compounds that have many biological and pharmacological activities and are exist in the structure many of natural products. Usually, synthesis of pyrrole derivatives by β‐nitrostyrene performed through multicomponent reactions. In this review, synthesis of pyrroles derivatives by β‐nitrostyrene through multicomponent reactions is discussed.
Inkjet‐Printing of Supercapacitors
Authors: Zub Karina , Winsberg Jan , Schubert Ulrich S. , Hoeppener Stephanie 
Published: September 2020

AbstractThe fabrication of supercapacitors and coin cells by means of inkjet printing based on the utilization of a commercially available graphite‐based ink is reported. The printing steps have been optimized utilizing a commercial office inkjet printer. Adjustments to the printing conditions as well as optimizing the device layout enabled the fabrication of usable supercapacitors and details of the assembly and processing steps have been investigated. Studies included a careful tuning of the ink properties to obtain homogeneous electrodes, to optimize layer thickness and, as a consequence, performance of the supercapacitor devices. Finally, the performance of the printing process was cross‐checked by the fabrication of a coin‐cell layout. Special emphasis was placed on the printing process to establish a simple and readily applicable fabrication of prototype device layouts.