bluuebunny/crossref_metadata_2025 huggingface dataset:
A Rare Case of Transesophageal Echocardiography Probe-Induced Tongue Ulcer
Authors: Surwade Sanjay , Chelani Ratan , Butani Manju
Published: December 2022

Transesophageal echocardiography (TEE) is a commonly used diagnostic and monitoring modality in anesthetic practice. It is used in neurosurgery for monitoring cardiac function and detecting venous air embolism. TEE is a semi-invasive procedure and is considered to be reasonably safe with a few complications. During neurosurgical cases, access to the head end is limited and TEE can cause injury due to prolonged contact. These injuries can be noticed only at the conclusion of the surgery. We report a rare case of tongue ulcer caused due to the use of TEE in a sitting neurosurgical procedure with a complete resolution.
Permanent First Mandibular Molar: Loss Prevalence and Pattern among Saudis in Al-Ahsa
Authors: Almahdi Hatim Mohammed , Alabdrabulridha Zuhair , AlAbbas Jawad , Saad Ali Albin , Alarka Ismail , Alghatm Sajjad , Alqasem Hadi
Published: December 2022

Objectives The permanent first mandibular molar (PFMM) is the first tooth to erupt, usually at the age of 6 years. It is the most effective oral masticatory unit due to its wide occlusal surface and its role in favorable occlusion. This study describes the prevalence of PFMM loss and the reasons for extraction in a group of King Faisal Dental Complex Clinics (KFUDC) Saudi attendees. In addition, to report postextraction complications, consider the gender, age, and the time elapsed from the moment of the extraction.

Materials and Methods A cross-sectional study was performed in January to April 2020, focusing on the loss of PFMM among a group of Saudis attending KFUDC in Al Hofuf, Saudi Arabia. A total of 417 participants were recruited. The inclusion criteria were adults aged ≥ 18 years. The principal investigator performed all the necessary measures for calibration in the forms of training on clinical examination and interviews.

Statistical Analysis Data were analyzed using the Statistical Package for the Social Science, version 25 (SPSS Inc., Illinois, United States).

Result Four hundred seventeen attendees participated in the present study. Majority were males 73.9% (308), and 26.1% (109) females. A third, 30% (125), reported missing PFMM; the overwhelming majority reported the reason for extraction as caries 93.6% (117).

On clinical examination, 80.8% (101) had complications; drifting of adjacent teeth was the most common complication, 57.6% (72), followed by supraeruption in 23.2% (29).

More males than females reported missing PFMM (22.8 and 7.2%, respectively), and those ≥ 25 years reported more missing PFMM than younger (17.5 and 12.5%, p ≤ 0.000). Those confirmed with systemic diseases reported more missing PFMM than their counterpart (23.3 and 6.7%, p ≤ 0.01).

Those with good oral hygiene reported less missing PFMM than their poor oral hygiene counterparts (27.8 and 34%). Those who had good knowledge about the complications of early extraction of PFMM stated less missing PFMM than their counterparts (15.6 and 14.4%, p ≤ 0.01).

Conclusion This study indicated that PFMM were the most common extracted tooth. Caries is the principal reason for tooth extraction among the studied population, followed by periodontal diseases. Emphasis on preventing dental caries is essential to maintain a socially and economically productive life and reduce the burden of oral disease.
Medical Treatment Options for Ulcerative Colitis
Authors: Sleiman Joseph , Bassi Mehak , Tsipotis Evangelos , Charabaty Aline
Published: December 2022

The landscape of management of ulcerative colitis, a type of inflammatory bowel disease, continues to change with advancement in pharmaceutical options as well as clinical treatment targets. Ulcerative colitis primarily involves the superficial layers of the large bowel, and cause active inflammation that can affect the colon from the rectum to the cecum in a relapsing and a remitting course. In this review, we provide evidence-based guidance on the selection of appropriate medical therapies based on individual patient and disease characteristics, with a focus on biologics and small molecules. We also review the role of surgery and management of acute severe ulcerative colitis.
Ultrasound Shear Wave Elastography of Normal Pancreas in Adult Subjects
Authors: Choudhury Shayeri Roy , Verma Mansi , Gupta Pankaj , Singh Harjeet , Sharma Vishal , Kochhar Rakesh
Published: December 2022

Background and Purpose Transabdominal ultrasound (US)-based shear wave elastography (SWE) provides an attractive method of estimating pancreatic stiffness. There is limited data on the SWE values of the healthy pancreas in Indian subjects. The current study aimed to evaluate SWE of the normal pancreas.

Methods We performed a study from January 2019 to March 2019. We included adult patients who presented for the US of the upper abdomen for vague abdominal symptoms, unrelated to the pancreas. The SWE values were obtained from the pancreatic head and body. The association of pancreatic SWE with age, gender, fatty liver, chronic liver disease, and cholelithiasis was recorded.

Results During the study period, 205 subjects underwent SWE of the pancreas. The mean age of subjects was 41.3 (standard deviation [SD] 15.3) years. There were 93 males and 112 females. The mean SWE value in the head of the pancreas was 8.98 (SD 2.46 kPa), and that in the body region was 8.67 (SD 2.67 kPa). There was a positive correlation of SWE with age. The SWE of the pancreatic body was significantly higher in patients who had a fatty liver on US (p < 0.05). There was no significant association of SWE of the pancreas with gender, presence of chronic liver disease, or gallstones.

Conclusion The normal values of pancreatic SWE are correlated with age and fatty change in the liver.
Novel Worm-like Micelles for Hydrochloride Doxorubicin Delivery: Preparation, Characterization, and In Vitro Evaluation
Authors: Yang Ya-Ni , Ge Chen , He Jun , Lu Wei-Gen
Published: December 2022

Doxorubicin hydrochloride (DOX) is one of the widely used antineoplastic agents in treating various cancers, yet it is always associated with the occurrence of adverse reactions that limit its clinical use. Currently, encapsulating DOX in micelles may represent a promising strategy to reduce toxicity and side effects of the drug. This study aimed to explore a novel acitretin-based surfactant (ACMeNa) with good solid stability to encapsulate DOX to form micelles (ACM-DOX). In this work, ACM-DOX micelles were prepared by a microfluidic method free of organic solvents. The characteristics of ACM-DOX micelles were assessed, including morphology, particle size, stability, entrapment efficiency, and drug loading. An in vitro cytotoxicity experiment of the micelles on MDA-MB-231 (a human breast cancer cell line) was also performed. The micelle formation mechanism suggested that the insoluble ACMeNa/DOX complex was formed by electrostatic interaction, and subsequently encapsulated by self-assembly into micelles. The designed ACM-DOX micelles had an average particle size of 19.4 ± 0.2 nm and a zeta potential of −43.7 ± 2.4 mV, with entrapment efficiency and drug loading efficiency of 92.4 ± 0.5% and 33.4 ± 0.3%, respectively. The ACM-DOX micelles had worm-like structures under a Cryo-transmission electron microscope and exhibited good stability within 8 hours after reconstitution and 4- to 32-fold dilution of its reconstituted solution. ACM-DOX micelles released 80% of DOX within 24 hours in a medium of pH = 5.0, and its drug profile can be described by a first-order model. Moreover, ACM-DOX micelles showed cytotoxicity against MDA-MB-231 in a dose-dependent manner, and displayed a higher antitumor activity as compared with free DOX, with IC50 values of DOX and ACM-DOX micelles being 6.80 ± 0.50 and 4.64 ± 0.32 μg/mL, respectively. Given above, ACMeNa has great application potential as a DOX carrier for the treatment of cancers.
Understanding the Acceptability of Health Apps among Adolescents: A Qualitative Study
Authors: Chen Elizabeth , Muessig Kathryn E. , Moracco Kathryn E.
Published: December 2022

Background Almost all adolescents aged 13 to 17 in the United States have access to a smartphone. While studies have commonly assessed the feasibility or usability of mobile health applications (“apps”), few have examined the acceptability of apps—whether individuals would actually use these health apps in their everyday lives—among adolescent populations.

Objectives This qualitative study aims to understand how adolescents assess the acceptability of health apps in the context of their everyday lives.

Methods Nineteen adolescents in grades 7 through 9 were asked to download a health app before participating in two semi-structured interviews 2 weeks apart. Seven domains from the Theoretical Framework of Acceptability were assessed: affective attitude, burden, ethicality, intervention coherence, opportunity costs, perceived effectiveness, and self-efficacy. A Grounded Theory approach was used to analyze data.

Results The seven acceptability domains plus two additional themes, intervention expectations (what adolescents anticipated given their experiences with other apps) and peer norms (friends' beliefs and attitudes toward the intervention's health topic), were salient.

Conclusion These nine domains of acceptability are relevant to adolescents and should be assessed during health app development by app developers and health researchers to improve adolescents' acceptability perceptions and potentially increase app usage.
Effectiveness of Psychosocial Intervention on Quality of Life of Mothers of Children with Cancer: A Feasibility Study
Authors: Chavan Seema S. , Mendonca Theresa L.
Published: December 2022

Background Mothers of children with cancer are reported to experience stress more often. For children with cancer, parents are the primary source of social and emotional support, and they are also in charge of how successfully patients manage their illness. The degree of difficulty parents suffer after learning that their child has cancer significantly influences the child's psychological adjustment.

Aim The study aimed to assess the effectiveness of psychosocial intervention on quality of life (QoL) among mothers of children with cancer.

Materials and Methods Quasi-intervention study design was undertaken, and a purposive sampling technique was used to select the 60 mothers of children with cancer who were assigned randomly to the intervention and control groups. A pretested and validated self-administered questionnaire was used; the sociodemographic, WHOQOL-BREF scale with 26 items was studied.

Statistical Analysis Prevalence, demographic pro forma of mother and child was analyzed in terms of frequency, percentage, mean, and standard deviation. Two-factor repeated measures analysis of variance was used to establish the effectiveness of the psychosocial intervention on QoL. Association was done by using the chi-square test. SPSS package was used for analysis.

Results Psychosocial intervention was found to be effective in improving QoL scores in psychological health domain (p = 0.02*, p < 0.05), social relationship domain (p = 0.04*, p < 0.05), and environmental health domain (p = 0.001**, p < 0.05). A significant association was found between the physical health domain and information on cancer (p = 0.01*), psychological health domain and financial status (p = 0.03*), social relationship domain and cost of treatment (p = 0.04*), Q1 and Q2 with the place of residence (p = 0.004**, p = 0.02*), and Q2 and financial status (p = 0.03*).

Conclusion Mothers of children with cancer undergo a lot of stress and emotional turmoil and are at risk of deteriorating their QoL. Hence, they need to be provided support to address their issues. Thus, health professionals must develop and implement interventions to promote the QoL.
Surgical and Interventional Management of Liver Metastasis
Authors: Itenberg Edwin R. , Lozano Ana M.
Published: December 2022

Colorectal cancer is one of the most common cancers diagnosed worldwide. While the incidence of colorectal cancer has been declining since the adoption of screening colonoscopy, the findings of liver metastasis are still found in up to 25% of patients at diagnosis. The management of liver metastasis has evolved over the past two to three decades, and survival rates have improved secondary to improved systemic therapy, surgical options, and local therapies. In this article, we aim to review the available surgical and ablative options for management of colorectal liver metastasis, as well as appropriate imaging and patient selection.
Building brand meaning in social entrepreneurship organizations: the social impact brand model
Authors: Lückenbach Florian , Schmidt Holger J. , Henseler Jörg
Published: December 2022

In the face of numerous complex challenges at the ecological, economic, and social levels, Social Entrepreneurship Organizations (SEOs) offer an approach that is both solution-oriented and future-oriented by combining profitability and purpose. However, the achievement of social goals is closely linked to the ability to operate successfully in competitive environments, in which differentiation strategies, in particular the creation of strong and authentic brands, are vital to survival. Although the new paradigm of brand management, the so-called co-creative paradigm, has been extensively researched in recent decades both in the for-profit and non-profit contexts, there is still scarce empirical research addressing the field of SEOs. To exploit the potential that the co-creation paradigm offers for SEOs, our paper introduces a social impact brand model (SIBM), which sheds new light on the design process of social entrepreneurial brand meaning. The findings identify key drivers in creating SEO brands by focusing on a dual-brand core that consists of an impact mission orientation and an entrepreneurial orientation, internal branding activities, the founder's personal brand, and relevant brand (co-)creators. By aligning their brand management activities with the SIBM, SEOs can create brands that have authentic and stable brand meanings while managing stakeholder groups' various expectations.
Economic experiments support Ostrom’s polycentric approach to mitigating climate change
Authors: Milinski Manfred , Marotzke Jochem
Published: December 2022

The late Nobel laureate Elinor Ostrom envisioned a polycentric approach to mitigating climate change rather than a centralised solution. Debating about global efforts to solve climate-change problems has yet not led to an effective global treaty. Ostrom argued that instead of focusing only on global efforts, it is better to encourage polycentric efforts to reduce the risks associated with the emission of greenhouse gases. Many problems conceptualised as ‘global problems’ are the cumulative results of actions taken by individuals, families, small groups, private firms, and local, regional, and national governments. Ostrom and colleagues pointed to many examples of successfully managing a common good through interaction within a community. Energy-saving actions undertaken by individuals, families and actors at a small-scale pay off and, when multiplied, may reduce emissions globally. The incentive to achieve an individual net gain may trigger human investment decisions. Here we provide experimental support for Ostrom’s basic ideas using methods of experimental economics. By subdividing experimental populations in subgroups that approach sub-goals of mitigating simulated dangerous climate change combined with incentives, the ‘global’ solution is achieved by combined subgroup contributions exceeding the ‘global’ threshold for averting simulated dangerous climate change. Incentives from refunded saved energy motivate reaching sub-goals, as Ostrom suggested. By contrast, coercing free-riding subgroups through sanctioning at a cost fails, because sanctioning also hits fair individuals who then reduce their contributions. However, the power of polycentricity with numerous successful units can help mitigate climate change.
The role of the electric field in the departure of vapor bubbles in microgravity
Authors: Bucci Mattia , Zupančič Matevž , Garivalis Alekos Ioannis , Sielaff Axel , Di Marco Paolo , Golobič Iztok
Published: December 2022

We present the results of a study aimed at investigating the effects of electric fields on quasi-static bubble departure dynamics during pool boiling of perfluorohexane (FC-72) in microgravity conditions. Analysis was performed through an alternative formulation of the bubble momentum balance in which the contribution of non-uniform electric stress distributions at the bubble interface can be quantified through high-speed video measurements without having to numerically solve the laws of electrostatics. Data used in this study were obtained in the scope of the Multiscale Boiling Project, which included advanced single bubble growth experiments performed aboard the International Space Station. Our results confirm that bubble departure counterintuitively begins before the force resulting from electric stresses starts to pull the bubble up from the wall. When this occurs, it is shown that the shrinking process of the contact line accelerates, in agreement with known theoretical results. It is concluded that the electric force is essentially determined by the electric stress distribution at the bubble cap above the contact area. Furthermore, we show that the electric stress at the bubble interface is also responsible for the increase in bubble internal overpressure, which explains the early departure of the bubble while increasing the intensity of the electric field. The results of this study provide an important step in achieving a more comprehensive understanding of the bubble behavior at the heated surface in the presence of an electric field, which is essential to optimally design electrodes and two-phase heat transfer devices for future space applications.
Collective transport of droplets through porous media
Authors: Coelho Rodrigo C. V. , Silva Danilo P. F. , Maschio António M. R. , Telo da Gama Margarida M. , Araújo Nuno A. M.
Published: December 2022

The flow of deformable particles, such as droplets, dragged by a fluid, through a network of narrow pores inside rocks or other porous media is key in a range of applications, from enhanced oil recovery and water filtration to lab on a chip sorting of cells. The collective dynamics and its impact on the flow are poorly understood. Here, using droplets as a prototype, we show that collective transport can occur for conditions under which a single particle would get trapped at a pore channel. When a series of droplets gets trapped, the fluid flow is affected significantly, leading to an increase of the pressure difference across the pore channels, which, in turn, squeezes the particles through the channels. We analyze the conditions for a single droplet to flow through one pore and derive the corresponding Bond number. We also obtain a rule for the collective flow of droplets in porous media.
An experimental study on the effects of wall heating on coherent structures in a turbulent boundary layer
Authors: Yuan Cheng , Dai Xingyu , Tian Wei
Published: December 2022

An experimental investigation was conducted for a better understanding of the turbulence behavior and the coherent structure in a turbulent boundary layer over a heated plate, which is horizontal facing upwards. To explore the effects of wall temperature on the turbulent boundary layer behavior, the boundary layer flow was observed at four different temperatures between the plate and inlet flow (δT=0, 15, 30, and 50 K), with the momentum Reynolds number of the inlet flow set to Reθ=1196. We show that based on the comparison of turbulent kinetic energy (TKE) distribution between unheated- and heated-wall cases, the wall-heated turbulent boundary layer can be divided into three regions, namely, the near-wall region, the intermediate region, and the outer region. The relationship between the TKE distribution and the coherent structures in each region is explored by comparing the detailed flow-field measurement results for the unheated- and heated-wall cases. In the near-wall region, the decrease in fluid viscosity caused by wall heating has stabilization effects on the turbulent fluctuation. With the increase in wall temperature, the streaky structures display a continuous decrease in their spanwise meandering and an increase in their streamwise coherency. The intermediate region ranges from the logarithmic region to the thermal boundary layer edge. The buoyant force caused by wall heating has a significant effect on the turbulence behavior in this region. Under the influence of buoyant force, the large-scale coherent structures for the wall-heating case were found to contain more kinetic energy and incline away from the wall with a larger angle, which leads to the increased TKE in the intermediate region for the wall-heating case. In the outer region, the occurrence of separated turbulent structures is measurably more common for the wall-heating case. Owing to the shedding of the turbulent structures from the turbulent production source (i.e., large-scale coherent structures originating from the near-wall region), the TKE in the outer region for the wall-heating case is less than that of the unheated case.
Magnetic-field-responsive property of Fe3O4/polyaniline solvent-free nanofluid
Authors: Huai Yulu , Hu Weipeng , Song Wenqi , Zheng Yaping , Deng Zichen
Published: December 2022

The fascinating liquid-like behavior of Fe3O4/polyaniline (Fe3O4/PANI) solvent-free nanofluid permits some important applications. However, for the lack of investigation on the magnetic response mechanism of the Fe3O4/PANI solvent-free nanofluid, the precise magnetic control on the liquid-like behaviors of the Fe3O4/PANI solvent-free nanofluid is difficult. Thus, the magnetic field response of the Fe3O4/PANI solvent-free nanofluid is investigated employing a complex structure-preserving approach in this paper. Considering one branch chain grafting on the Fe3O4/PANI nanoparticle, a flexible hub-beam model is proposed. The dynamic equations of the flexible magnetic hub-beam model subjected to the external magnetic field force and the viscous resistance are deduced in the Lagrangian framework. Combing the symplectic precise integration method and the generalized multi-symplectic method, a complex structure-preserving approach is developed to study the magnetic field response characteristics of the Fe3O4/PANI solvent-free nanofluid. From the numerical results, the upper limit of the stable moving speed of the Fe3O4/PANI solvent-free nanofluid is obtained. In addition, the effects of the model parameters (including the external magnetic field strength as well as the length of the branch chain) on the upper limit of the stable moving speed of the Fe3O4/PANI solvent-free nanofluid are analyzed. The above results can be used to guide the magnetic control strategy design for the rheological property of the magnetic solvent-free nanofluid.
Multiphysics modeling of femtosecond laser–copper interaction: From electron dynamics to plasma eruption
Authors: Zhan Ningwei , Guo Baoshan , Jiang Lan , Zhang Tianyong , Chen Meiling , Lin Gen
Published: December 2022

The femtosecond laser ablation of metals is a complex and violent nonequilibrium process, and numerous studies have sought to reveal the evolution of a single physical phenomenon, such as laser-induced periodic surface micro-nanostructures or plasma eruptions. By considering the multiphysics scenarios of energy and heat transfer, structural mechanics, hydrodynamics, and nucleation dynamics, a femto-nanosecond and nano-micrometer multiscale framework combining electron–phonon-coupled heat transfer, lattice deformation, phase transition, and plasma eruption was constructed to describe the heat and mass transfer mechanism of femtosecond laser–copper interaction. A multiphysics model was proposed in this study to simulate the ablation process with different laser fluences. Ablation occurs at low near-threshold fluences primarily via a combination of the thermal phase transition process of melting and thermoplastic deformation coupled with the nonthermal phase transition process of hot electron explosion. Marangoni convection and non-uniform nucleation at the solid–liquid interface create micro-nano structures on the surface of the ablation crater. At a high laser fluence, plasma plumes are emitted via gasification and eruption, and as the material is heated to decrease its density, the surface is broken into a micro-column structure, and then the micro-columns fracture and erupt to form micro-nano structures and plasma plumes. Numerical results offer a better understanding of surface topography modifications and plasma plume evolution and promote the application of femtosecond laser precision fabrication in the fields of aviation, mechanics, electronics, and materials engineering.
Flow-mediated interaction between a forced-oscillating cylinder and an elastically mounted cylinder in less regular regimes
Authors: Lin Zhonglu , Liang Dongfang , Zhao Ming
Published: December 2022

This study investigates the interaction between an actively oscillating cylinder and a passive cylinder elastically mounted with a damper. Both cylinders are rigid, immersed in a viscous fluid, of the same diameter and constrained to move along the two cylinders' centerline. This problem is simulated by an in-house finite-element solver. Six non-dimensional groups are chosen as input: the active cylinder's frequency f1/fn=0.05−3.2 and amplitude A1/D=0.159−1.432, the passive cylinder's damping ratio ζ=0, 0.02 and mass ratio m*=2, the Reynolds number Rem=35−315, and gap distance G/D=2.5. The resulting Keulegan–Carpenter and the Stokes numbers are KC=1−9 and β=35. In total, 2176 combinations are studied in this parametric space. An increase in KC leads to higher irregularity and larger vibration amplitude of the passive cylinder. In regime C, the passive cylinder vibrates in a pulse-beating pattern due to the periodic switching of the streaming direction. In regime E, the passive cylinder responds with intermittent irregularity. In regime F, the flow structure switches intermittently among unrecognizable irregularities and three regular patterns resembling those observed in regimes C and E. In regime G, the flow is highly irregular and circular, where vortices shed from consecutive cycles can merge, forming a much larger one.
A mesoscale bubble-induced turbulence model and simulation of gas–liquid flows
Authors: Jiao Yunpeng , Wang Limin , Chen Jianhua
Published: December 2022

In gas–liquid two-phase flows, bubble motion significantly affects liquid phase turbulence, and adding bubble-induced turbulence (BIT) source term is widely used to improve the simulation accuracy. This paper presents a new BIT model based on the energy-minimization multi-scale (EMMS) methodology. The model was constructed by considering two mesoscale factors, i.e., the sub-grid structures through analyzing the slip velocity and the gas holdup gradient, and the equivalent diameter of turbulent eddies calculated by the EMMS-based turbulence model. In order to verify its performance, the model was incorporated to the Eulerian–Lagrangian simulating framework and applied to two typical experimental systems. Both mean flow characteristics and turbulence quantities were well predicted, and the new model showed advantages over traditional BIT models, especially at higher gas velocities. Moreover, a strategy for counting energy dissipation in the simulation was devised and performed whereby the dual effects of promotion and suppression on liquid phase turbulence by bubbles can be reflected. The simulations demonstrated that BIT dominated the energy dissipation and turbulence was enhanced by BIT at higher gas velocities, while shear-induced turbulence dominated the energy dissipation and turbulence is reduced due to the suppression by bubbles at lower gas velocities.
The ascidian Lissoclinum patella, the patellamides and copper
Authors: Baur Philipp , Comba Peter , Gahan Lawrence R. , Scholz Christian
Published: December 2022

The ascidian species Lissoclinum patella is found, amongst other places, around Heron Island on the Great Barrier Reef, Australia. L. patella has a cyanobacterial symbiont, Prochloron didemni, known to produce various cyclic peptides, including quantities of the cyclic pseudo-octapeptides, the patellamides. Patellamides are of pharmaceutical interest and have attracted the curiosity of coordination chemists because they can form quite stable mono- and di-nuclear transition metal complexes, particularly with copper(ii). For some patellamide derivatives, the binding of two CuII centres is cooperative and solution equilibria involving metal-free peptides, mono- and di-nuclear copper(ii) complexes, and various functions of these complexes have been described. These studies were also driven by the observation that the ascidians possess copper concentrations in excess of that in the seawater around Heron Island, and accumulation factors of approximately 104 have repeatedly been reported. New data presented here, based on inductively coupled plasma atomic emission spectroscopy (ICP-OES) and ICP-mass spectromety (MS) measurements, indicate that the 104 factor is overestimated and a factor >500 and up to approximately 3000 is more realistic.
Aerosol variability and glacial chemistry over the western Himalayas
Authors: Rashid Irfan , Bhat Imtiyaz Ahmad , Najar Nadeem Ahmad , Kang Shichang , Jan Faisal Zahoor , Dar Shahid Ahmad , Bhat Sami Ullah , Kashani Syed Danish Rafiq , Rasool Waseem
Published: December 2022

Environmental context While it is known that aerosol deposition causes exacerbated melt of the glaciers, information about aerosol variability and deposition in the glaciated environments in the western Himalayas is still lacking. We analysed the aerosol variability, modelled the potential aerosol sources and assessed physicochemical characteristics of glacier ice in the region. This information could be foundational for initiating studies on aerosol impacts on the glacier melt besides climate change. Rationale There is increasing scientific evidence of aerosol deposition triggering glacier melting but very little understanding about the spatiotemporal variability of aerosols over the Indian Himalayas. The current study is a maiden effort to ascertain the aerosol variability in glacial environments of the Indian Himalayas. Aerosol sources were modelled and physicochemical characteristics of glacial ice were evaluated to draw firsthand insights into the light-absorbing impurities over three glaciers. Methodology Aerosol variability over four decades was analysed using MERRA-2 data (Modern-Era Retrospective analysis for Research and Applications) over five different topographically distinct mountain ranges of the western Himalayas. Information about nine physicochemical variables was analysed over the ablation zone of glaciers in the region. HYSPLIT model was used to track the air mass sources at a weekly time-step from December 2020 to November 2021 over the selected glaciers. Results and discussion MERRA-2 data analyses indicate increasing trends in surface dust, columnar dust and black carbon. The highest columnar dust concentration was found in Pir Panjal Mountain Range (PP: 125 648 µg m−2) followed by the Greater Himalayan Mountain Range of Kashmir (GH: 64 384 µg m−2), Karakoram (KA: 47 574 µg m−2), Ladakh (LA: 45 861 µg m−2) and Zanskar (ZA: 38 416 µg m−2), however, the black carbon indicated a PP > GH > LA > KA > ZA trend. HYSPLIT trajectories indicate that the contribution of global sources is highest (65%) followed by local (21%) and regional (14%) sources. Ice chemistry analysis revealed a higher concentration of total solid particles (830 mg L−1) and sulfates (14.33 mg L−1) indicative of the contribution from anthropogenic footprint and lithology. Conclusion The research underpins the need for establishing long-term aerosol observatories and a detailed hydrochemical assessment for precisely ascertaining the black carbon and allied constituents to unravel their contribution to glacier melt in the north-western Himalayas.
Application of CRISPR-Based Human and Bacterial Ribosomal RNA Depletion for SARS-CoV-2 Shotgun Metagenomic Sequencing
Authors: Cerón Stacey , Clemons Nathan C , von Bredow Benjamin , Yang Shangxin
Published: December 2022

Objectives

The aim of this study is to evaluate the effectiveness of a CRISPR-based human and bacterial ribosomal RNA (rRNA) depletion kit (JUMPCODE Genomics) on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shotgun metagenomic sequencing in weakly positive respiratory samples.

Methods

Shotgun metagenomics was performed on 40 respiratory specimens collected from solid organ transplant patients and deceased intensive care unit patients at UCLA Medical Center in late 2020 to early 2021. Human and bacterial rRNA depletion was performed on remnant library pools prior to sequencing by Illumina MiSeq. Data quality was analyzed using Geneious Prime, whereas the identification of SARS-CoV-2 variants and lineages was determined by Pangolin.

Results

The average genome coverage of the rRNA-depleted respiratory specimens increased from 72.55% to 93.71% in overall samples and from 29.3% to 83.3% in 15 samples that failed to achieve sufficient genome coverage using the standard method. Moreover, rRNA depletion enhanced genome coverage to over 85% in 11 (73.3%) of 15 low viral load samples with cycle threshold values up to 35, resulting in the identification of genotypes.

Conclusion

The CRISPR-based human and bacterial rRNA depletion enhanced the sensitivity of SARS-CoV-2 shotgun metagenomic sequencing, especially in low viral load samples.
Clinical Significance of Perineural Invasion by Prostate Cancer Detected on Needle Core Biopsy
Authors: Teramoto Yuki , Numbere Numbereye , Wang Ying , Miyamoto Hiroshi
Published: December 2022

Objectives

The clinical impact of the laterality of perineural invasion (PNI) by prostate cancer remains poorly understood. We herein compared radical prostatectomy (RP) findings and long-term oncologic outcomes in patients with prostate cancer with PNI in two prostate biopsy (PBx) sites.

Methods

We retrospectively assessed 170 consecutive patients undergoing systematic sextant PBx where PNI had been detected in two of six PBx sites, followed by RP.

Results

PNI occurred unilaterally in 140 (82.4%) cases and bilaterally in 30 (17.6%) cases. Compared with unilateral PNI, bilateral PNI was significantly associated with a higher number of cancer-positive sites and longer total tumor length on PBx. However, there were no significant differences in RP findings, including tumor grade/stage and tumor volume, between unilateral and bilateral PNI cohorts. Kaplan-Meier analysis revealed that patients with bilateral PNI had a significantly higher risk of disease progression after RP than those with unilateral PNI (P = .038). In multivariate analysis, bilateral PNI (vs unilateral PNI) showed significance for progression (hazard ratio, 2.281; P = .023).

Conclusions

In PBx specimens exhibiting PNI in two sextant sites, bilateral PNI was found to be associated with poorer prognosis as an independent predictor but not worse histopathologic features in RP specimens compared with unilateral PNI.
Morphologic Characteristics and Mutational Analysis of Fumarate Hydratase Deficient Kidney and Smooth Muscle Tumors
Authors: McMurtry Valarie , Mahlow Jonathan , Coleman Joshua F , Deftereos Georgios , Jattani Rakhi , Bastien Roy R L , Durtschi Jacob , Jarboe Elke , Lomo Lesley , Sirohi Deepika
Published: December 2022

Objectives

Fumarate hydratase (FH)–deficient tumors can occur due to germline or somatic mutations and have distinctive morphologic features. The aims of this study are to refine morphologic criteria and identify mutations in FH-deficient smooth muscle tumors (SMTs).

Methods

The morphology of SMTs and kidney tumors submitted to a national reference laboratory for FH immunohistochemistry (IHC) was reviewed by two gynecologic and two genitourinary pathologists, respectively. Fisher exact test was used for analysis. Fourteen SMTs were sequenced using the Illumina TruSight Oncology 500 Assay.

Results

Twenty-two kidney tumors (5 FH deficient) and 51 SMTs (27 FH deficient) were reviewed. FH-deficient kidney tumors exclusively showed cord-like growth, rhabdoid change, and absence of coagulative tumor necrosis and psammoma bodies. FH-deficient SMTs were significantly more likely to have staghorn vessels, eosinophilic cytoplasmic inclusions, schwannoma-like areas, or hereditary leiomyomatosis and renal cell cancer–like nuclei (P < .05 for each). Seven of 14 sequenced SMTs showed mutations of the FH gene and no other driver mutations.

Conclusions

FH-deficient SMTs submitted for FH immunohistochemistry (IHC) showed distinct morphology. Although FH IHC is used for screening of FH-deficient tumors, FH mutations were identified in only 50% of FH-deficient SMTs. This highlights the need for additional exploration of mechanisms of FH protein loss in tumors lacking FH mutations.
WHO Laboratory Biosafety Manual: A New Approach to Security
Authors: Ficociello Barbara , Giordano Daniela , Incoronato Federica , Farinella Andrea , Pietrangeli Biancamaria
Published: December 2022

The paper aims to highlight the new indications introduced in the 4th edition of the “Laboratory Biosafety Manual” of World Health Organization. The authors propose a new vision to improve biosafety and biosecurity in the laboratory aligned with the technical standards ISO 35001:2019 “Biorisk management for laboratories and other related organizations” and ISO 45001:2018 “Occupational health and safety management systems—Requirements with guidelines for use” framework. The current edition has a more innovative approach compared to the previous ones, more attention is given to training awareness and providing skills, to promote the culture of safety by adopting an approach based on risk analysis, rather than the prescriptive approach that has been used previously.
The British Association of Aesthetic Plastic Surgeons (BAAPS) Gluteal Fat Grafting Safety Review and Recommendations
Authors: Tillo Omar , Nassab Reza , Pacifico Marc D
Published: December 2022

Superficial gluteal lipofilling is a fat grafting procedure performed to correct a trochanteric depression and buttock deflation. Brazilian butt lift (BBL) is a gluteal lipofilling procedure traditionally associated with exaggerated appearance and intramuscular fat transfer. The risk of mortality from fat embolism in BBL was previously reported as being 1:2500. The actual risk was later estimated to be nearer 1:15,000, which is similar to the mortality risk in abdominoplasty. There is increasing evidence regarding the safety of subcutaneous gluteal lipofilling. This has principally been related to new technologies, surgical techniques, and training being developed to avoid intramuscular injection of fat. The efficacy and benefits of intraoperative ultrasound for guiding the subcutaneous placement of fat and avoiding inadvertent deep lipofilling have been demonstrated. Other serious risks and complications must be considered in addition to mortality. These include hypothermia, sepsis, skin necrosis, and poor aesthetic results, as well as the much-publicized risk of fat embolism. Complications are better controlled and managed in strictly regulated healthcare settings. Patients seeking surgery at unregulated facilities or via medical tourism are deemed to be at higher risk of being exposed to these serious complications and/or inadequate subsequent management.
Hericium erinaceuspolysaccharide improves the microstructure, immune function, proliferation and reduces apoptosis of thymus and spleen tissue cells of immunosuppressed mice
Authors: Han Yujiao , Huang Jialiang , Zhao Chunfang , Zhang Feng , Gu Youfang , Wang Chenfang , Jin Erhui
Published: December 2022

In order to study the effect of Hericium erinaceus polysaccharide (HEP) on the immune and antioxidation functions of immunosuppressed mice. The control group received distilled water orally and the model and experimental groups I, II, and III received 0, 80, 160, and 320 mg/kg HEP respectively for a fortnight after re-molding with cyoclphosphnalide (CTX). Compared with the control group, the secretion of IL-2, IL-4, and IFN-γ, the activity or content of T-AOC, T-SOD, and GSH-PX, and the expression of PCNA mRNA in the thymus and spleen were reduced in immunosuppressed mice (P < .05 or P < .01). Compared with immunosuppressed mice, the levels of IL-2, IFN-γ, and GSH-PX and the PCNA mRNA expression of spleen and thymus were increased (P < .05 or P < .01), and the microstructure were also obviously improved in the experimental group III. Overall, 320 mg/kg of HEP significantly improved the immune and antioxidant functions.
Avoidance behavior and experience-dependent tolerance in response to bitter compounds inCaenorhabditis elegans
Authors: Ishikawa Seiryu , Iida Chiharu , Takezawa Yuka , Chiba Kyoko , Kage-Nakadai Eriko
Published: December 2022

This study investigates the mechanisms governing experience-dependent tolerance of bitter compounds in Caenorhabditis elegans. The nematodes showed an aversion to nicotinamide, MgCl2, isoleucine, and arginine in a Gα-dependent manner. Worms furthermore displayed diminished avoidance of MgCl2 upon MgCl2-preconditioning at the larval stages. AIY interneurons have been suggested to be involved in experience-dependent behavioral plasticity.
GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data
Authors: Kim Minsoo , Vo Daniel D , Kumagai Michi E , Jops Connor T , Gandal Michael J
Published: December 2022

With the continued deluge of results from genome-wide association and functional genomic studies, it has become increasingly imperative to quickly combine and visualize different layers of genetic and genomic data within a given locus to facilitate exploratory and integrative data analyses. While several tools have been developed to visualize locus-level genetic results, the limited speed, scalability and flexibility of current approaches remain a significant bottleneck. Here, we present a Julia package for high-performance genetics and genomics-related data visualization that enables fast, simultaneous plotting of hundreds of association results along with multiple relevant genomic annotations. Leveraging the powerful plotting and layout utilities from Makie.jl facilitates the customization and extensibility of every component of a plot, enabling generation of publication-ready figures.

Availability and implementation

The GeneticsMakie.jl package is open source and distributed under the MIT license via GitHub (https://github.com/mmkim1210/GeneticsMakie.jl). The GitHub repository contains installation instructions as well as examples and documentation for built-in functions.

Supplementary information

Supplementary data are available at Bioinformatics online.
Variable-selection ANOVA Simultaneous Component Analysis (VASCA)
Authors: Camacho José , Vitale Raffaele , Morales-Jiménez David , Gómez-Llorente Carolina
Published: December 2022

Motivation

ANOVA Simultaneous Component Analysis (ASCA) is a popular method for the analysis of multivariate data yielded by designed experiments. Meaningful associations between factors/interactions of the experimental design and measured variables in the dataset are typically identified via significance testing, with permutation tests being the standard go-to choice. However, in settings with large numbers of variables, like omics (genomics, transcriptomics, proteomics and metabolomics) experiments, the ‘holistic’ testing approach of ASCA (all variables considered) often overlooks statistically significant effects encoded by only a few variables (biomarkers).

Results

We hereby propose Variable-selection ASCA (VASCA), a method that generalizes ASCA through variable selection, augmenting its statistical power without inflating the Type-I error risk. The method is evaluated with simulations and with a real dataset from a multi-omic clinical experiment. We show that VASCA is more powerful than both ASCA and the widely adopted false discovery rate controlling procedure; the latter is used as a benchmark for variable selection based on multiple significance testing. We further illustrate the usefulness of VASCA for exploratory data analysis in comparison to the popular partial least squares discriminant analysis method and its sparse counterpart.

Availability and implementation

The code for VASCA is available in the MEDA Toolbox at https://github.com/josecamachop/MEDA-Toolbox (release v1.3). The simulation results and motivating example can be reproduced using the repository at https://github.com/josecamachop/VASCA/tree/v1.0.0 (DOI 10.5281/zenodo.7410623).

Supplementary information

Supplementary data are available at Bioinformatics online.
LapTrack: linear assignment particle tracking with tunable metrics
Authors: Fukai Yohsuke T , Kawaguchi Kyogo
Published: December 2022

Motivation

Particle tracking is an important step of analysis in a variety of scientific fields and is particularly indispensable for the construction of cellular lineages from live images. Although various supervised machine learning methods have been developed for cell tracking, the diversity of the data still necessitates heuristic methods that require parameter estimations from small amounts of data. For this, solving tracking as a linear assignment problem (LAP) has been widely applied and demonstrated to be efficient. However, there has been no implementation that allows custom connection costs, parallel parameter tuning with ground truth annotations, and the functionality to preserve ground truth connections, limiting the application to datasets with partial annotations.

Results

We developed LapTrack, a LAP-based tracker which allows including arbitrary cost functions and inputs, parallel parameter tuning and ground-truth track preservation. Analysis of real and artificial datasets demonstrates the advantage of custom metric functions for tracking score improvement from distance-only cases. The tracker can be easily combined with other Python-based tools for particle detection, segmentation and visualization.

Availability and implementation

LapTrack is available as a Python package on PyPi, and the notebook examples are shared at https://github.com/yfukai/laptrack. The data and code for this publication are hosted at https://github.com/NoneqPhysLivingMatterLab/laptrack-optimisation.

Supplementary information

Supplementary data are available at Bioinformatics online.
Oocyte quality evaluation: a review of engineering approaches toward clinical challenges
Authors: Palay Peyman , Fathi Davood , Fathi Rouhollah
Published: December 2022

Although assisted reproductive technology has been very successful for the treatment of infertility, its steps are still dependent on direct human opinion. An important step of assisted reproductive treatments in lab for women is choosing an oocyte that has a better quality. This step would predict which oocyte has developmental competence leading to healthy baby. Observation of the oocyte morphological quality indicators under microscope by an embryologist is the most common evaluation method of oocyte quality. Such subjective method which relies on embryologist’s experience may vary and leads to misdiagnosis. An alternative solution to eliminate human misjudging in traditional methods and overcome the limitations of them is always using engineering-based procedure. In this review article, we deeply study and categorize engineering-based methods applied for the evaluation of oocyte quality. Then, the challenges in laboratories and clinics settings move forward with translational medicine perspective in mind for all those methods which had been studied were discussed. Finally, a standardized process was presented, which may help improving and focusing the research in this field. Moreover, effective suggestion techniques were introduced that are expected they would be complementary methods to accelerate future researches. The aim of this review was to create a new prospect with the engineering approaches to evaluate oocyte quality and we hope this would help infertile couples to get a baby.