bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helical Structures for Medical Applications
Authors: Eldeeb M , Mattar H , Hatem H , Elmahdy D , Shanan N , Elwi M , Klingner A , Ramzy A 
Published: October 2020

Abstract
The latest advances in the field of microrobotics assisted medical experts in the treatment of some of human diseases especially intravascular diseases such as atherosclerosis. In this research, a phantom for the atherosclerotic plaque material is fabricated using Gelatine and Nano Hydroxyapatite in a catheter tube to mimic the condition in the human body in vitro. For plaque penetration a helical microrobot is designed to achieve the optimum plaque clearing efficiency. The robot is a remotely controlled micro helical magnetic based metallic robot which is inserted in the catheter to penetrate the phantom by rotational motion along its axis. The motion of the robot during mechanical grinding of the plaque phantom is simulated using MATLAB where the distance of the robot’s journey inside the plaque phantom is plotted against the time consumed by the robot.
Blue, Red, and Green Emission from Chromium and Copper Metal Doped Lithium Borate Glass
Authors: Kashif I. , Ratep A. 
Published: October 2020

Abstract
The influence of copper metal on the structural and optical properties (absorption and emission) of the lithium borate glass samples containing chromium considered. The analysis of FTIR spectra measured, indicated the copper and chromium ions act as network former and modifier depend on the concentration of everyone in the sample content. The ratio between the BO4 groups to the total boron groups (BO4+BO3) decreases with the copper content increases up to 2 mol % and then increase. The optical properties that the Dq/B decreases with the increase the copper and higher than 2.3 which indicates the glass samples containing Cr3+ions in the high-field sites and produce conventional laser action. The emission spectra show the intensity emission bands at 440 nm, 540 nm, and 730 nm for relative strong blue, green and red bands respectively.
Optical and Thermophysical Characterization of Fe3O4nanoparticle
Authors: Horia F , Easawi Khaled , Khalil Reda , Abdallah Said , El-Mansy Mabrouk , Negm Sohair 
Published: October 2020

AbstractThe size dependence of optical and, thermophysical properties of Fe3O4nanoparticle (NPs) has been investigated. Three samples of Fe3O4NPs with different sizes were prepared by the Co-precipitation method and labeled a, b and c. The UV- vis spectra shifted toward the lower energy with increasing the particles size. The energy bandgaps of the synthesized Fe3O4NPs are 1.84 ev,1,73 ev, and 1,47 ev for a, b and c respectively. The sizes of the nanoparticles were estimated using the effective mass approximation (EMA) model, and are 10.7 nm, 20.56 nm, and 30.43 nm. These values are comparable to those found by transmission electron microscope (TEM) and X-ray diffraction (XRD). The Photoacoustic (PA) technique was used to research Fe3O4NPs for thermal diffusivity (α), thermal effusivity (e), and thermal conductivity (k). The determined values of α, e, and k increase as the size of nanoparticles rises and decreases from the bulk by about 33%.
Strong exciton-photon coupling in large area MoSe2 and WSe2 heterostructures fabricated from two-dimensional materials grown by chemical vapor deposition
Authors: Gillard Daniel J , Genco Armando , Ahn Seongjoon , Lyons Thomas P , Yeol Ma Kyung , Jang A-Rang , Severs Millard Toby , Trichet Aurélien A P , Jayaprakash Rahul , Georgiou Kyriacos , Lidzey David G , Smith Jason M , Suk Shin Hyeon , Tartakovskii Alexander I 
Published: October 2020

Abstract
Two-dimensional semiconducting transition metal dichalcogenides embedded in optical microcavities in the strong exciton-photon coupling regime may lead to promising applications in spin and valley addressable polaritonic logic gates and circuits. One significant obstacle for their realization is the inherent lack of scalability associated with the mechanical exfoliation commonly used for fabrication of two-dimensional materials and their heterostructures. Chemical vapor deposition offers an alternative scalable fabrication method for both monolayer semiconductors and other two-dimensional materials, such as hexagonal boron nitride. Observation of the strong light-matter coupling in chemical vapor grown transition metal dichalcogenides has been demonstrated so far in a handful of experiments with monolayer molybdenum disulfide and tungsten disulfide. Here we instead demonstrate the strong exciton-photon coupling in microcavities composed of large area transition metal dichalcogenide/hexagonal boron nitride heterostructures made from chemical vapor deposition grown molybdenum diselenide and tungsten diselenide encapsulated on one or both sides in continuous few-layer boron nitride films also grown by chemical vapor deposition. These transition metal dichalcogenide/hexagonal boron nitride heterostructures show high optical quality comparable with mechanically exfoliated samples, allowing operation in the strong coupling regime in a wide range of temperatures down to 4 Kelvin in tunable and monolithic microcavities, and demonstrating the possibility to successfully develop large area transition metal dichalcogenide based polariton devices.
Talking about public good for the second quantum revolution: analysing quantum technology narratives in the context of national strategies
Authors: Roberson Tara , Leach Joan , Raman Sujatha 
Published: October 2020

AbstractThe ‘second quantum revolution’ has been the subject of substantial speculation, investment by public and private sectors, and media hype. We investigate some of this hype in the form of three national strategies for quantum technology. In the course of analysing these strategies, we ask: how can we ensure new quantum technologies benefit the societies they are used in and are a part of ? To help clarify this question, we posit a public good test for quantum research requiring diversity in research agendas, social orders, and research-society networks.
Optimal FPE for non-linear 1d-SDE. I: Additive Gaussian colored noise
Authors: Bianucci Marco , Mannella Riccardo 
Published: October 2020

Abstract
Many complex phenomena occurring in physics, chemistry, biology, finance, etc can be reduced, by some projection process, to a 1-d stochastic Differential equation (SDE) for the variable of interest. Typically, this SDE is both non-linear and non-Markovian, so a Fokker Planck equation (FPE), for the probability density function (PDF), is generally not obtainable. However, a FPE is desirable because it is the main tool to obtain relevant analytical statistical information such as stationary PDF and First Passage Time. This problem has been addressed by many authors in the past, but due to an incorrect use of the interaction picture (the standard tool to obtain a reduced FPE) previous theoretical results were incorrect, as confirmed by direct numerical simulation of the SDE. The pitfall lies in the rapid diverging behavior of the backward evolution of the trajectories for strong dissipative flows. We will show, in general, how to address this problem and we will derive the correct best FPE from a cumulant-perturbation approach. The specific perturbation method followed gives general validity to the results obtained, beyond the simple case of exponentially correlated Gaussian driving used here as an example: it can be applied even to non Gaussian drivings with a generic time correlation.
Stratified Mucin Producing Intraepithelial Lesion (SMILE): Report of Two Cases
Authors: Bellamkonda V , Avalos Hernandez S R , Dal Zotto V 
Published: October 2020

Abstract

Introduction/Objective
Stratified mucin producing intraepithelial lesion (SMILE) is an uncommon variant of adenocarcinoma in-situ (AIS), often confused with immature squamous metaplasia or high-grade intraepithelial lesion (HG-SIL). This premalignant lesion is often found in proximity to HG-SIL, AIS and invasive carcinomas. SMILE is also a precursor for Invasive Stratified Mucinous Carcinoma. As was first described in the original article, SMILE lesions are considered derived from the reserve cells at the transformation zone where HPV infections lead to varied phenotypes.

Methods
Two cases of SMILE were collected from our files. A 31-year-old female with a previous abnormal Pap smear result. She underwent cervical biopsy and subsequent LEEP.The second patient, a 26-year-old female, underwent a cervical biopsy after an abnormal Pap smear.

Results
Histologically, stratified cells with presence of conspicuous mucin production with abundant cytoplasm separating cells in mid and lower layer of epithelium accompanied with conspicuous spacing of nuclei in the lower to middle epithelial layer are seen. Additionally, there is nuclear pleomorphism with absence of gland formation.
Mucicarmine stain was performed and showed positive staining in mucin producing dysplastic cells throughout the epithelium. Immunoperoxidase stains demonstrated positivity for p16 (nuclear and cytoplasmic) and p63 in the basal cells. The Ki67 proliferation index was high (approximately 90%). These results supported the diagnostic interpretation of SMILE.

Conclusion
SMILE is a rare variant of glandular precursor lesion in the cervix. It is frequently associated with HG-SIL and/or AIS, but may rarely appear as an isolated finding. The differential diagnosis include adenocarcinoma in-situ, atypical immature squamous metaplasia and squamous intraepithelial lesion. Since these lesions are cervical glandular intraepithelial neoplasms, the morphologic recognition of a SMILE in a biopsy is important for patient follow up, particularly in cases were only squamous intraepithelial lesion is present in the sample.
Primary Pulmonary NUT Carcinoma with NSD3-NUTM1 Fusion
Authors: Khan J , Whaley R , Cheng L 
Published: October 2020

Abstract
Casestudy: NUT carcinoma is a rare poorly differentiated carcinoma that is highly aggressive and resistant to multiple treatment modalities. It is estimated to represent 0.6% of non-glandular lung carcinomas. The undifferentiated morphology presents a challenge in arriving at the correct diagnosis, especially on biopsy specimens. Since its original description in 2004, the demographics are shifting to include older individuals and non-midline structures due to the broader availability of ancillary studies. Classically, NUT carcinoma harbors a t(15;19)(q14;p13.1) resulting in the BRD4- NUTM1 fusion gene while other fusion partners are rare. We present a case of primary pulmonary NUT carcinoma with a NSD3-NUTM1 (WHSC1L1-NUTM1) fusion in a 78-year-old male. The patient was lifelong nonsmoker with no significant past medical history who presented with abdominal pain. Imaging revealed 1.4 cm nodule in the right lower lobe. Subsequent biopsy revealed a poorly differentiated squamous cell carcinoma. The neoplastic cells expressed positivity for p40 while lacking expression of TTF1, CK7, CK20, and chromogranin. Resection and lymph node dissection revealed a highly cellular neoplasm composed of epithelioid cells with variable amounts of faintly eosinophilic cytoplasm. Focal keratinization was apparent. The nuclei were plump, vesicular, and fairly uniform with variably prominent nucleoli. Metastatic disease was present in 5 of 5 mediastinal lymph nodes. Adjuvant chemotherapy was planned and next generation sequencing was performed. A NSD3-NUTM1 (WHSC1L1-NUTM1) fusion was discovered and was followed with NUT immunohistochemistry which displayed the characteristic speckled nuclear pattern. Thus refining the original diagnosis to NUT carcinoma. Chemotherapy consisted of cisplatin- gemcitabine and carboplatin-gemcitabine. At last follow-up (7 months) he is alive with no evidence of disease. This case highlights the importance of familiarity with NUT carcinoma and including this rare disease in the differential diagnosis in patients who are lifelong nonsmokers with poorly differentiated lung carcinomas.
Should CD138 Immunohistochemistry be Standard Recommended Practice for Bone Marrow Evaluation of Plasma Cell Neoplasms?
Authors: Vijayanarayanan A , Inamdar K , Menon M , Kuriakose P 
Published: October 2020

Abstract

Introduction/Objective
Myeloma diagnosis by a pathologist requires 10% plasma cells (PC) or a biopsy proven plasmacytoma in addition to myeloma defining events. PC% &gt; 60% is a biomarker of malignancy under this definition. WHO allows for assesment of plasma cell percentage either by aspirate count or by CD138 immunohistochemistry (IHC). There is lack of consensus on aspirate smear adequacy for PC% estimation. Uneven distribution of plasma cells, hemodilution and/or patchy infiltration can lead to gross underestimation. We compared PC% by aspirate count and CD138 IHC and established corelation with serum protein electrophoresis (SPEP) values.

Methods
67 myeloma cases were included after excluding cases with suboptimal or inadequate aspirate smears. Two hematopathologists evaluated the diagnostic marrow (therapy naive) for PC% by aspirate count and CD138 IHC on biopsy/clot section. Corresponding SPEP and Free light chain (FLC) values were obtained. Correlation coefficent was calculated using Pearson correlation coefficient (GraphPad Prism).

Results
The Ig subtypes included IgG (41/67) and IgA (17/67). 12 cases had available FLC values. Both average and median PC% by CD138 IHC was considerably higher (50%, 52%) compared to aspirate count (29%, 21%). However, PC% by aspirate smear count and CD138 IHC demonstrated a significant linear correlation (r=0.71, p60% by CD138 (and not by aspirate count).

Conclusion
CD138 IHC based PC% is consistently higher, nevertheless, statistically significant linear corelation is observed between aspirate count PC% and CD138 IHC. A significant linear correlation is observed between CD138 IHC and SPEP (IgG and IgA), however, no such correlation is observed with aspirate count. More cases were diagnosed as myeloma (11%) and higher propotion of cases (35%) had biomarker of malignancy i.e. PC% &gt;60% by CD138 IHC. Based on these findings, we propose estimation of PC% by CD138 immunostain be a recommended standard practice for better clinicopathologic and biologic correlation.
Error Reduction in Specimen Processing of Irretrievable Body Fluids
Authors: Gannon V , Albright T , Wells T , Cahak C , Harrington A M , Buchan B , Ledeboer N , Kloc W 
Published: October 2020

Abstract

Introduction/Objective
A lack of standardized processes for laboratory handling of irretrievable body fluid specimens, such as cerebrospinal fluid, serous fluids, synovial fluids, and aspirates, can result in failures that put the patient at risk by delaying testing results and/or requiring specimen recollection. We noted increased patient safety issues with irretrievable specimens in our laboratory and implemented a process improvement plan to mitigate patient harm.
Herein, we report our findings of this intervention.

Methods
A task force was organized with wide representation across the laboratory to design a new workflow for irretrievable specimens. Hospital Patient Safety Reporting data was used to identify flaws in the pre-analytical processes pre-intervention and to monitor effectiveness of process change, post-intervention. Our intervention consisted of developing a standardized pre-analytical process for both technical and non-technical staff that could be enforced through consistent and proper training, with well-defined responsibilities for each department involved including specimen processing, microbiology, hematology, and chemistry. Our process included a centralized sterile processing location within the Micro department as well as a standardized sample log in and sample distribution process that incorporated a chain of custody form.

Results
Pre-intervention, we had 23 patient safety reports during a 3-month period (5-10/month; average 8/month) on irretrievable specimens; post-intervention, we had 9 patient safety reports over a 5-month period (0-4/month; average 2/month). Pre-intervention, failures identified included inconsistent workflows and training among staff, the absence of established protocols, and inadequate communication. Post-intervention, failures were noted due to improper and inconsistent training (n=4) or deviation from the established procedure by staff members. These failures were investigated and addressed through retraining or corrective actions as needed.

Conclusion
Our data shows that the implementation of a standardized process within the laboratory significantly decreases patient safety events by improving testing turn-around-times and quality of results and by preventing the need for specimen recollections.
iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak
Authors: Wei Zhiting , Gao Yuli , Meng Fangliangzi , Chen Xin , Gong Yukang , Zhu Chenyu , Ju Bin , Zhang Chao , Liu Zhongmin , Liu Qi 
Published: October 2020

Abstract
Emerging viral infections seriously threaten human health globally. Several challenges exist in identifying effective compounds against viral infections: (1) at the initial stage of a new virus outbreak, little information, except for its genome information, may be available; (2) although the identified compounds may be effective, they may be toxic in vivo and (3) cytokine release syndrome (CRS) triggered by viral infections is the primary cause of mortality. Currently, an integrative tool that takes all those aspects into consideration for identifying effective compounds to prevent viral infections is absent. In this study, we developed iDMer, as an integrative and mechanism-driven response system for addressing these challenges during the sudden virus outbreaks. iDMer comprises three mechanism-driven compound identification modules, that is, a virus-host interaction-oriented module, an autophagy-oriented module and a CRS-oriented module. As a one-stop integrative platform, iDMer incorporates compound toxicity evaluation and compound combination identification for virus treatment with clear mechanisms. iDMer was successfully tested on five viruses, including the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our results indicated that, for all five tested viruses, compounds that were reported in the literature or experimentally validated for virus treatment were enriched at the top, demonstrating the generalized effectiveness of iDMer. Finally, we demonstrated that combinations of the individual modules successfully identified combinations of compounds effective for virus intervention with clear mechanisms.
Calibrating variant-scoring methods for clinical decision making
Authors: Benevenuta Silvia , Capriotti Emidio , Fariselli Piero 
Published: October 2020

Abstract

Summary
Identifying pathogenic variants and annotating them is a major challenge in human genetics, especially for the non-coding ones. Several tools have been developed and used to predict the functional effect of genetic variants. However, the calibration assessment of the predictions has received little attention. Calibration refers to the idea that if a model predicts a group of variants to be pathogenic with a probability P, it is expected that the same fraction P of true positive is found in the observed set. For instance, a well-calibrated classifier should label the variants such that among the ones to which it gave a probability value close to 0.7, approximately 70% actually belong to the pathogenic class. Poorly calibrated algorithms can be misleading and potentially harmful for clinical decision making.

Avaliability and implementation
The dataset used for testing the methods is available through the DOI:10.5281/zenodo.4448197.

Supplementary information
Supplementary data are available at Bioinformatics online.
A robust computational pipeline for model-based and data-driven phenotype clustering
Authors: Simoni Giulia , Kaddi Chanchala , Tao Mengdi , Reali Federico , Tomasoni Danilo , Priami Corrado , Azer Karim , Neves-Zaph Susana , Marchetti Luca 
Published: October 2020

Abstract

Motivation
Precision medicine is a promising field that proposes, in contrast to a one-size-fits-all approach, the tailoring of medical decisions, treatments or products. In this context, it is crucial to introduce innovative methods to stratify a population of patients on the basis of an accurate system-level knowledge of the disease. This is particularly important in very challenging conditions, where the use of standard statistical methods can be prevented by poor data availability or by the need of oversimplifying the processes regulating a complex disease.

Results
We define an innovative method for phenotype classification that combines experimental data and a mathematical description of the disease biology. The methodology exploits the mathematical model for inferring additional subject features relevant for the classification. Finally, the algorithm identifies the optimal number of clusters and classifies the samples on the basis of a subset of the features estimated during the model fit. We tested the algorithm in two test cases: an in silico case in the context of dyslipidemia, a complex disease for which a large population of patients has been generated, and a clinical test case, in the context of a lysosomal rare disorder, for which the amount of available data was limited. In both the scenarios, our methodology proved to be accurate and robust, and allowed the inference of an additional phenotype division that the experimental data did not show.

Availability and implementation
The code to reproduce the in silico results has been implemented in MATLAB v.2017b and it is available in the Supplementary Material.

Supplementary information
Supplementary data are available at Bioinformatics online.
MiRKAT: kernel machine regression-based global association tests for the microbiome
Authors: Wilson Nehemiah , Zhao Ni , Zhan Xiang , Koh Hyunwook , Fu Weijia , Chen Jun , Li Hongzhe , Wu Michael C , Plantinga Anna M 
Published: October 2020

Abstract

Summary
Distance-based tests of microbiome beta diversity are an integral part of many microbiome analyses. MiRKAT enables distance-based association testing with a wide variety of outcome types, including continuous, binary, censored time-to-event, multivariate, correlated and high-dimensional outcomes. Omnibus tests allow simultaneous consideration of multiple distance and dissimilarity measures, providing higher power across a range of simulation scenarios. Two measures of effect size, a modified R-squared coefficient and a kernel RV coefficient, are incorporated to allow comparison of effect sizes across multiple kernels.

Availability and implementation
MiRKAT is available on CRAN as an R package.

Supplementary information
Supplementary data are available at Bioinformatics online.