bluuebunny/crossref_metadata_2025 huggingface dataset:
A cluster randomized controlled trial for a multi-level, clinic-based smoking cessation program with women in Appalachian communities: study protocol for the “Break Free” program
Authors: Patterson Joanne G. , Borger Tia N. , Burris Jessica L. , Conaway Mark , Klesges Robert , Ashcraft Amie , Hauser Lindsay , Clark Connie , Wright Lauren , Cooper Sarah , Smith Merry C. , Dignan Mark , Kennedy-Rea Stephenie , Paskett Electra D. , Anderson Roger , Ferketich Amy K.
Published: February 2022

Background

The cervical cancer burden is high among women living in Appalachia. Cigarette smoking, a cervical cancer risk factor, is also highly prevalent in this population. This project aims to increase smoking cessation among women living in Appalachia by embedding a smoking cessation program within a larger, integrated cervical cancer prevention program.

Methods

The broader program, the Take CARE study, is a multi-site research collaborative designed to address three risk factors for cervical cancer incidence and mortality: tobacco use, human papillomavirus (HPV) infection, and cervical cancer screening. Break Free is a primary care clinic-based implementation program that aims to promote smoking cessation among female smokers in Appalachia by standardizing clinical practice protocols. Break Free includes: (1) implementation of a tobacco user identification system in the Electronic Health Record, (2) clinic staff and provider training on the Ask, Advise and Refer (AAR) model, (3) provider implementation of AAR to identify and treat women who want to quit smoking within the next 6 months, (4) facilitated access to cessation phone counseling plus pharmacotherapy, and (5) the bundling of Break Free tobacco cessation with HPV vaccination and cervical cancer screening interventions in an integrated approach to cervical cancer prevention. The study spans 35 Appalachian health clinics across 10 healthcare systems. We aim to enroll 51 adult female smokers per health system (total N = 510). Baseline and follow-up data will be obtained from participant (provider and patient) surveys. The primary outcome is self-reported 12-month point prevalence abstinence among enrolled patients. All randomized patients are asked to complete follow-up surveys, regardless of whether they participated in tobacco treatment. Data analysis of the primary aims will follow intent-to-treat methodology. Secondary outcomes will assess program implementation and cost effectiveness.

Discussion

Addressing high tobacco use rates is critical for reducing cervical cancer morbidity and mortality among women living in Appalachia. This study evaluates the implementation and effectiveness of a smoking cessation program in increasing smoking cessation among female smokers. If results demonstrate effectiveness and sustainability, implementation of this program into other health care clinics could reduce both rates of smoking and cervical cancer.

Trial registration NCT04340531 (April 9, 2020)
Reconstruction clipping of ruptured anterior circulation aneurysms via supraorbital lateral keyhole approach
Authors: Wu Yuzhang , Zhao Yan , Yu Shengping , Li Fan , Cai Shifei , Peng Chao , Wang Zhen , Yang Yifan , Wang Bangyue , Yang Xinyu
Published: February 2022

Background

Intracranial aneurysm (IA) is a serious disease. Analyze and review the cases of anterior circulation ruptured IA by supraorbital lateral keyhole approach, and summarize the experiences of this approach.

Methods

Retrospective analysis of 16 cases of ruptured anterior circulation IA in our department from January 2019 to June 2020, CT angiography (CTA) was performed before operation. Analyzing the IA’s parameters by 3D-CT reconstruction. The IA was clipped by supraorbital lateral keyhole approach combined with the 3D-skull reconstruction. Extraventricular drainage was performed before craniotomy. Intraoperative neurophysiological monitoring was performed during the operation. After operation, fluorescein angiography and vascular ultrasound were performed to check the clipping effect. Intracranial pressure monitor was performed postoperatively. CTA was reexamined one week after operation. The modified Rankin Scale (MRS) was performed 6 months after operation.

Results

There were 7 males (43.8%) and 9 females (56.2%), and the average age is 52.31 ± 11.12 years old. Among them, 11 patients (68.8%) were anterior communicating artery aneurysms and 5 (31.2%) were middle cerebral artery aneurysms. All patients were out of hospital within 10 days without any death, without cerebral infarction, cerebrospinal fluid leakage and neurological impairments. About mRS score, after 6 months follow-up, 8 cases (50%) had 0 point, 4 cases (25%) had 1 point, and 4 cases (25%) had 2 points.

Conclusions

For ruptured anterior circulation IA, the supraorbital lateral keyhole approach combined with ventricular drainage, intraoperative electrophysiological monitoring, and intraoperative vascular ultrasound is a safe and minimally invasive treatment. The application of reconstruction clipping can reconstruct the diameter of parent vessel and reduce the recurrence rate of IA.
Using combined environmental–clinical classification models to predict role functioning outcome in clinical high-risk states for psychosis and recent-onset depression
Authors: Antonucci Linda A. , Penzel Nora , Sanfelici Rachele , Pigoni Alessandro , Kambeitz-Ilankovic Lana , Dwyer Dominic , Ruef Anne , Sen Dong Mark , Öztürk Ömer Faruk , Chisholm Katharine , Haidl Theresa , Rosen Marlene , Ferro Adele , Pergola Giulio , Andriola Ileana , Blasi Giuseppe , Ruhrmann Stephan , Schultze-Lutter Frauke , Falkai Peter , Kambeitz Joseph , Lencer Rebekka , Dannlowski Udo , Upthegrove Rachel , Salokangas Raimo K. R. , Pantelis Christos , Meisenzahl Eva , Wood Stephen J. , Brambilla Paolo , Borgwardt Stefan , Bertolino Alessandro , Koutsouleris Nikolaos ,   the PRONIA Consortium
Published: February 2022

Background

Clinical high-risk states for psychosis (CHR) are associated with functional impairments and depressive disorders. A previous PRONIA study predicted social functioning in CHR and recent-onset depression (ROD) based on structural magnetic resonance imaging (sMRI) and clinical data. However, the combination of these domains did not lead to accurate role functioning prediction, calling for the investigation of additional risk dimensions. Role functioning may be more strongly associated with environmental adverse events than social functioning.

Aims

We aimed to predict role functioning in CHR, ROD and transdiagnostically, by adding environmental adverse events-related variables to clinical and sMRI data domains within the PRONIA sample.

Method

Baseline clinical, environmental and sMRI data collected in 92 CHR and 95 ROD samples were trained to predict lower versus higher follow-up role functioning, using support vector classification and mixed k-fold/leave-site-out cross-validation. We built separate predictions for each domain, created multimodal predictions and validated them in independent cohorts (74 CHR, 66 ROD).

Results

Models combining clinical and environmental data predicted role outcome in discovery and replication samples of CHR (balanced accuracies: 65.4% and 67.7%, respectively), ROD (balanced accuracies: 58.9% and 62.5%, respectively), and transdiagnostically (balanced accuracies: 62.4% and 68.2%, respectively). The most reliable environmental features for role outcome prediction were adult environmental adjustment, childhood trauma in CHR and childhood environmental adjustment in ROD.

Conclusions

Findings support the hypothesis that environmental variables inform role outcome prediction, highlight the existence of both transdiagnostic and syndrome-specific predictive environmental adverse events, and emphasise the importance of implementing real-world models by measuring multiple risk dimensions.
A Successful Model for an Introductory Oncology Teaching Conference and Its Impact on Preclinical and Clinical Medical Students
Authors: Kanan Duaa , Kanan Tarek , Kalyenci Nursena , Nanah Abdel Rahman , Tarbaghia Marwa , Ekmekci Betigul , Çelik Serkan , Öven Bala Başak
Published: February 2022

PURPOSE:

Oncology education at medical schools is often fragmented, under-represented, and nonstandardized. Medical students lack essential knowledge, skills, and attitudes necessary for them to provide optimal primary care to patients with cancer upon graduation.

METHODS:

In this study, we designed and assessed the impact of a compact oncology teaching conference on medical students. The conference covered topics in cancer biology, public health, diagnosis, patient management, treatment, and communication skills. Medical students completed voluntary presurveys and postsurveys regarding their perceived knowledge, attitudes, and perspectives. The event was promoted by student groups, particularly our ASCO Oncology Student Interest Group, and took place online.

RESULTS:

A total of 228 responses from medical students representing 50 universities were analyzed. We revealed significant baseline confidence and perceived knowledge deficits especially in diagnosis and patient management, and treatment modalities. Our conference positively affected self-assessed knowledge acquisition among students, with the most pronounced differences seen in diagnosis and patient management (2.51 ± 1 v 3.87 ± 0.81) and treatment modalities (2.54 ± 0.96 v 3.79 ± 0.88), P < .001. Students believed the program was beneficial, felt more confident in applying their knowledge in the clinic and in delivering bad news, and were more interested in pursuing oncology-related fields, P < .001.

CONCLUSION:

We demonstrated that a compact teaching conference resulted in significant improvements in students' confidence and perceived knowledge about oncology. Our successful teaching model can be adapted and implemented at medical schools globally. Development and evaluation of teaching programs are important to urgently reform undergraduate medical education in oncology.
Problems of Transition of Small and Medium-Sized Companies to New Accounting Standards
Authors: Zaharov K.
Published: February 2022

The article is devoted to the process of transition of small and medium-sized enterprises to the Federal Accounting Standards. On the basis of a survey conducted among the employees of small and medium-sized companies the author defined the major issues which the companies adopting the new standards have to deal with. The article provides a forecast of how the implementation of the new standards will be carried out.
Association between anxiety and sleepiness in medical students of the University of Guadalajara
Authors: González Heredia Tonatiuh , González Heredia Omar Nahum , Hernández Corona Diana Mercedes , González-Ramírez Leivy Patricia , Vázquez Jáuregui Adriana Iveth , Valle Reyes Araceli , Aguilar Alarcón Mónica Daniela
Published: February 2022

Introduction: Medical students could potentially be considered as a vulnerable group in terms of increased risk for anxiety and sleep disorders. This could be caused by high academic demands, and high levels of stress. There is little information, however, when it comes to the relationship between anxiety and excessive daytime sleepiness among medical students, and the potentially negative effects this relationship could have upon student health and academic performance. The objective was to identify the association between anxiety and excessive daytime sleepiness in medical students of the University of Guadalajara (Mexico). Materials and methods: A cross-sectional study was carried out, evaluating 173 students between January and April of 2019. The Epworth Sleepiness Scale was used for the determination of excessive daytime sleepiness, while the anxiety symptoms were measured using the Beck Anxiety Inventory. According to the cut-off points for the Epworth scales, the cut-off point was from 10 and for the Beck anxiety inventory it was 8. Chi square and Fisher’s exact test were used for statistical analysis. A value of p<0.05 was considered statistically significant. Results: Statistically significant differences were found between the students when comparing the presence and absence of excessive daytime sleepiness and anxiety with a value of p = 0.036 and Odds Ratio of 2.161. Conclusion: A high prevalence of anxiety and insomnia was found in the group of medical students which was evaluated. Additionally, it was found that students who suffer fromanxiety are more likely to develop excessive daytime sleepiness.
Condiciones socioambientales y prevalencia de enfermedades de piel en un asentamiento urbano precario de Asunción, Paraguay
Authors: Merino Iván , Fernández Paloma , Rodero Paloma
Published: February 2022

Introducción: En este artículo se analiza la influencia de las condiciones socioambientales de un asentamiento urbano precario de Asunción sobre la prevalencia de enfermedades dermatológicas que afectan a su población. Materiales y Métodos: Para ello, se realizó un estudio descriptivo y transversal con una muestra por cuotas que incluyó a 77 personas de entre 5 meses a 76 años de un slum. Resultados: Un 96.2 % de las personas presentó en el momento del examen físico al menos una lesión cutánea, un 79.2 % al menos una enfermedad infecciosas de piel, sin embargo, un 77.9 % no había recurrido a consulta médica. La exposición a un clima subtropical de altas temperaturas y húmedo, una alta relación de convivientes en el hogar por dormitorio, los problemas de provisión de agua y los suelos de arena en los hogares, así como un sistema de evacuación de excretas deficiente, la presencia de animales con escasa vigilancia sanitaria, la proximidad a arroyos depositarios de materia cloacal, y el impacto recurrente de raudales los días de intensa lluvia se relacionaron especialmente con el hallazgo de enfermedades cutáneas infecciosas, especialmente de etiología bacteriana (forunculosis y pioderma). Conclusión: Estas condiciones socioambientales se expresaron como factores relevantes a tener en cuenta para mejorar la atención a la salud de enfermedades dermatológicas de la población urbana que habita en un slum.
Visibility and Peer Influence in Durable Good Adoption
Authors: Bollinger Bryan , Gillingham Kenneth , Kirkpatrick A. Justin , Sexton Steven
Published: February 2022

This paper assesses the role of visibility as a channel for social influence in solar panel adoption.
Predictive Modelling: An Assessment Through Validation Techniques
Authors: Jeelani M. Iqbal , Danish Faizan , Khan Saquib
Published: February 2022

In this investigation, various statistical models were fitted on simulated symmetric and asymmetric data. Fitting of models was carried out with the help of various libraries in R studio, and various selection criteria were also used while fitting of models. In order to evaluate different validation techniques the simulated data was divided in training and testing data set and various functions in R were developed for the purpose of validation. Coefficient summary revealed that all statistical models were statistically significant across both symmetric as well as asymmetric distributions. In preliminary analysis TFEM (Type First Exponential Model) was found out to be the best linear model across both symmetric and asymmetric distributions with lower values of RMSE, MAE, BIAS, AIC and BIC. Among non-linear models, Haung model was found out to be best model across both the distributions as it has lower values of RMSE, MAE etc. Different validation techniques were used in the present study. Lower rates of prediction error in comparison to its counter parts, 5-folded cross validation performed better across all the statistical models.
Short Communication: Analysis of purity and concentration of DNA extracted from intron patho gene-spin extraction on crab processed food product samples
Authors: Sophian Alfi , PURWANINGSIH RATNA , MUINDAR MUINDAR , IGIRISA EKA PUTRI JUNIARTI , AMIRULLAH MUHAMMAD LUTHFI
Published: February 2022

Abstract. Sophian A, Purwaningsih R, Muindar, Igirisa EPJ, Amirullah ML. 2021. Short Communication: Analysis of purity and concentration of DNA extracted from intron patho gene-spin extraction on crab processed food product samples. Asian J Trop Biotechnol 18: 28-31. The purpose of this study was to optimize the Intron patho gene-spin DNA/RNA extraction kit on crab processed food products so that it can be used for testing samples other than viral and bacterial samples. The method used in purity and concentration analysis to analyze total DNA (yield) is the absorbance method using a nanophotometer and the method used to isolate the sample DNA is the centrifuge Column or spin column method. The research data showed that the extracted sample concentration was in the range of 15.15-15.75, with an average of 15.46. while the purity values measured at the A260/A280 wavelengths were obtained with a purity range between 2,124-2,346. The total DNA analysis (yield) results obtained an average of 755.04 with the lowest yield value of 575.50 and the highest yield value of 787.50. As a suggestion for further research, it is hoped that modification can be made to perfect the isolated DNA so that it has better purity and concentration values.
Short Communication: Agroforestry as sustainable agroecosystem in terrestrial semi-arid region, Indonesia: Evidence from soil organic carbon
Authors: Melinda Moata , TAKALAPETA AYDAM MEEL
Published: February 2022

Abstract. Moata MRS, Takalapeta AM. 2021. Short Communication: Agroforestry as sustainable agroecosystem in terrestrial semi-arid region, Indonesia: Evidence from soil organic carbon. Intl J Trop Drylands 5: 1-4. Agroforestry system has been recognized as a better system for food security, especially during dry season in a tropical region. Therefore, the sustainability of this system becomes crucial for rural livelihood, especially in dryland areas. One indicator for sustainable agriculture system is the total amount and quality of the soil organic matter (SOM) which is expressed as soil organic carbon (C-org). Therefore, this study focused on soil quality of three land uses (forest, dryland agriculture with less input, and agroforestry) under Inceptisol, Entisol, and Alfisol from 36 locations at dryland terrestrial ecosystem in West Timor-Indonesia. The results showed that all soils are dominated by clay and silt loam textures (54%) and neutral pH (83%) but still have very low SOM and C-org < 1% (48%). However, a mixed cropping system (agroforestry) provides a higher C-org compound (5% C-org) than other land uses (< 1% C-org). Carbon has a strong correlation with nitrogen (r=0.90, p= 0.0004), weak correlation with potassium (r= 0.51, p= 0,13) and correlation with phosphorus-P (r= 0.30, p = 0.40). The SOM in these terrestrial ecosystems has a moderate correlation with Cation Exchange Capacity (CEC) (r= 0,64, p = 0.04). It is indicated that most of the soil nutrients and CEC were influenced by SOM (C-org) except P (likely from mineral soil). It is a promising finding that agroforestry is a sustainable system for agriculture where SOM could be key driver for land productivity in the terrestrial ecosystem.
Delivery at Catholic hospitals and postpartum contraception use, five US states, 2015–2018
Authors: Menegay Michelle C. , Andridge Rebecca , Rivlin Katherine , Gallo Maria F.
Published: February 2022

Objectives

To evaluate whether the prevalence of postpartum contraceptive use was lower among people who delivered at a Catholic hospital compared to a non‐Catholic hospital.

Methods

We linked 2015–2018 Pregnancy Risk Assessment Monitoring System (PRAMS) survey data from five states to hospital information from the corresponding birth certificate file. People with a live birth self‐reported their use of contraception methods on the PRAMS survey at 2–6 months postpartum, which we coded into two dichotomous (yes vs. no) outcomes for use of female sterilization and highly‐effective contraception (female/male sterilization, intrauterine device, implant, injectable, oral contraception, patch, or ring). We conducted multilevel log‐binomial regression to examine the relationship between birth hospital type and postpartum contraception use adjusting for confounders.

Results

Prevalence of female sterilization for people who delivered at a Catholic hospital was 51% lower than that of their counterparts delivering at a non‐Catholic hospital (adjusted prevalence ratio: 0.49; 95% confidence interval: 0.37–0.65).

Conclusion

We found lower use of postpartum female sterilization, but no difference in highly effective contraception overall, for people who delivered at a Catholic hospital compared to a non‐Catholic hospital.
Nonlinear estimation of pressure projection of ultrasound fields in background-oriented schlieren imaging
Authors: Koponen Eero , Leskinen Jarkko , Tarvainen Tanja , Pulkkinen Aki
Published: February 2022

Background-oriented schlieren imaging is a recently proposed method for measuring projections of ultrasound fields. The method is based on observing deflection of light in a heterogeneous refractive index field that is induced by ultrasound via an acousto-optic effect. The deflection of light manifests as apparent perturbations in an imaged target, forming a potential flow estimation problem. In this work, the potential flow approach is formulated as a nonlinear regularized least-squares approach to alleviate limitations of approaches that linearize the problem. The nonlinear approach is shown to outperform the linear one when estimating projections of medically relevant ultrasound fields.
Flexible and transparent broadband microwave metasurface absorber based on multipolar interference engineering
Authors: Luo Yi , Huang Lirong , Ding Jifei , Liu Wenbing , Sun Bing , Xie Chenkai , Yang Helin , Wu Jiong
Published: February 2022

Electromagnetic multipoles enable rich electromagnetic interactions in a metasurface and offer another degree of freedom to control electromagnetic responses. In this work, we design and experimentally demonstrate an optically transparent, flexible and broadband microwave metasurface absorber based on multipolar interference engineering. Different from previous works, the designed metasurface simultaneously supports fundamental electric dipole and high-order electric quadrupole mode, whose interference satisfies the back-scattering suppression condition based on the generalized Kerker effect and thus high absorption. The measurement results indicate that the fabricated metasurface exhibits a high average absorption of 89% in the microwave band from 4 GHz to 18 GHz, together with a good optical transparency. Our study offers an alternative approach for designing broadband microwave metasurface absorber, which is potentially applicable in electromagnetic shielding, radar stealth and energy harvesting.
Real-time observation of chaotic and periodic explosions in a mode-locked Tm-doped fiber laser
Authors: Zeng Junjie , Sander Michelle Y.
Published: February 2022

We experimentally characterize the dynamics of soliton explosions in a transient chaotic state between a single and double pulsing state, as well as periodic explosions induced by soliton collisions in a dual wavelength soliton state. These explosions occurring in a thulium-doped linear fiber laser with net anomalous dispersion are characterized with real-time measurements based on a modified time-stretched dispersive Fourier transform method relying on second-harmonic generation.
Broadband terahertz guided-mode resonance filter using cyclic olefin copolymer
Authors: Bark Hyeon Sang , Park Mun-Won , Baek In Hyung , Jang Kyu-Ha , Jeong Young Uk , Lee Kitae , Jeon Tae-In
Published: February 2022

We propose an all-dielectric single-layer guided-mode resonance filter (GMRF) operating in the high-frequency terahertz (THz) region. For the fabrication of thin gratings to achieve strong resonance in the high-frequency region, the refractive index and absorption must be small, while the tensile strength must be high. Cyclic olefin copolymer (COC) films have a lower refractive index and absorption than polyethylene terephthalate (PET) films and a higher tensile yield strength than polytetrafluoroethylene (PTFE) films. Therefore, the COC film was found suitable to fabricate a GMRF operating in the high-frequency THz region. We fabricated COC-based single-layer GMRFs with a thickness of 50 µm and grating periods of 500, 400, 300, 200, and 100 µm; the resonance frequencies of the TE0,1 mode were 0.576, 0.712, 0.939, 1.329, and 2.759 THz, respectively. A shorter grating period caused a greater shift of the resonance to a higher frequency. In particular, the COC film enabled the fabrication of a 100-µm grating period with a ridge width of 32 µm and length of 2 mm, enabling the GMRF to operate up to 2.759 THz, which is very high frequency compared to the previous highest frequency of 0.7 THz. These results were in good agreement with a simulation using rigorous coupled-wave analysis.
Rapid simulations of hyperspectral near-field images of three-dimensional heterogeneous surfaces – part II
Authors: Chen Xinzhong , Yao Ziheng , Sun Zhiyuan , Stanciu Stefan G. , Basov D. N. , Hillenbrand Rainer , Liu Mengkun
Published: February 2022

The modeling of the near-field interaction in the scattering-type scanning near-field optical microscope (s-SNOM) is rapidly advancing, although an accurate yet versatile modeling framework that can be easily adapted to various complex situations is still lacking. In this work, we propose a time-efficient numerical scheme in the quasi-electrostatic limit to capture the tip-sample interaction in the near field. This method considers an extended tip geometry, which is a significant advantage compared to the previously reported method based on the point-dipole approximation. Using this formalism, we investigate, among others, nontrivial questions such as uniaxial and biaxial anisotropy in the near-field interaction, the relationship between various experimental parameters (e.g. tip radius, tapping amplitude, etc.), and the tip-dependent spatial resolution. The demonstrated method further sheds light on the understanding of the contrast mechanism in s-SNOM imaging and spectroscopy, while also representing a valuable platform for future quantitative analysis of the experimental observations.
Dynamic ellipsometry measurement based on a simplified phase-stable dual-comb system
Authors: Zhang Ruixue , Shi Liheng , Zhou Siyu , Zhang Jinxu , Liu Bin , Wu Guanhao
Published: February 2022

Spectroscopic ellipsometry is a powerful tool for characterizing thin film, polarization optics, semiconductors, and others. Conventional approaches are subject to restrictions of mechanical instability and measurement speed. The complex locking scheme of previous dual-comb spectroscopic ellipsometry belies its practicability. We present and demonstrate here dynamic spectroscopic ellipsometry based on a simplified phase-stable dual-comb system, which could realize the online dynamic measurement of optical properties of materials. A precision of 1.31 nm and a combined uncertainty of 13.80 nm (k = 2) in the thickness measurement of thin-film samples has been achieved. Moreover, the dynamic performance of the system is investigated under a high data acquisition rate (1 kHz) with a dynamic resolution of ellipsometric parameter better than 0.1 rad.
Nonlinear optical response of inverse-designed integrated photonic devices
Authors: Chen Hao , Zhang Ziming , Wang Guoqing , Shang Zhenyuan , Li Jiatong , Zhao Zexing , Zhang Mengyu , Guo Kai , Yang Junbo , Yan Peiguang
Published: February 2022

Gradient-based optimization combined with the adjoint method has been demonstrated to be an efficient way to design a nano-structure with a vast number of degrees of freedom. However, most inverse-designed photonic devices are applied as linear photonic devices. Here, we demonstrate the nonlinear optical response in inverse-designed integrated splitters fabricated on a SiN platform. The splitting ratio is tunable under different incident powers. The thermo-optical effect can be used as an effective approach for adjusting the nonlinear optical response threshold and modulation depth of the device. These promising results indicate the great potential of inverse-designed photonic devices in nonlinear optics and optical communications.
gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support
Authors: Irrgang M. Eric , Davis Caroline , Kasson Peter M.
Published: February 2022

Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is enabled by default in current versions of the software. Here we describe gmxapi 0.3 and later. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, the API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages.
Mitochondrial fusion regulates proliferation and differentiation in the type II neuroblast lineage in Drosophila
Authors: Dubal Dnyanesh , Moghe Prachiti , Verma Rahul Kumar , Uttekar Bhavin , Rikhy Richa
Published: February 2022

Optimal mitochondrial function determined by mitochondrial dynamics, morphology and activity is coupled to stem cell differentiation and organism development. However, the mechanisms of interaction of signaling pathways with mitochondrial morphology and activity are not completely understood. We assessed the role of mitochondrial fusion and fission in the differentiation of neural stem cells called neuroblasts (NB) in the Drosophila brain. Depleting mitochondrial inner membrane fusion protein Opa1 and mitochondrial outer membrane fusion protein Marf in the Drosophila type II NB lineage led to mitochondrial fragmentation and loss of activity. Opa1 and Marf depletion did not affect the numbers of type II NBs but led to a decrease in differentiated progeny. Opa1 depletion decreased the mature intermediate precursor cells (INPs), ganglion mother cells (GMCs) and neurons by the decreased proliferation of the type II NBs and mature INPs. Marf depletion led to a decrease in neurons by a depletion of proliferation of GMCs. On the contrary, loss of mitochondrial fission protein Drp1 led to mitochondrial clustering but did not show defects in differentiation. Depletion of Drp1 along with Opa1 or Marf also led to mitochondrial clustering and suppressed the loss of mitochondrial activity and defects in proliferation and differentiation in the type II NB lineage. Opa1 depletion led to decreased Notch signaling in the type II NB lineage. Further, Notch signaling depletion via the canonical pathway showed mitochondrial fragmentation and loss of differentiation similar to Opa1 depletion. An increase in Notch signaling showed mitochondrial clustering similar to Drp1 mutants. Further, Drp1 mutant overexpression combined with Notch depletion showed mitochondrial fusion and drove differentiation in the lineage, suggesting that fused mitochondria can influence differentiation in the type II NB lineage. Our results implicate crosstalk between proliferation, Notch signaling, mitochondrial activity and fusion as an essential step in differentiation in the type II NB lineage.
TOR complex 2 contributes to regulation of gene expression via inhibiting Gcn5 recruitment to subtelomeric and DNA replication stress genes
Authors: Cohen Adiel , Pataki Emese , Kupiec Martin , Weisman Ronit
Published: February 2022

The fission yeast TOR complex 2 (TORC2) is required for gene silencing at subtelomeric regions and for the induction of gene transcription in response to DNA replication stress. Thus, TORC2 affects transcription regulation both negatively and positively. Whether these two TORC2-dependent functions share a common molecular mechanism is currently unknown. Here, we show that Gad8 physically interacts with proteins that regulate transcription, including subunits of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex and the BET bromodomain protein Bdf2. We demonstrate that in the absence of TORC2, Gcn5, the histone acetyltransferase subunit of SAGA, accumulates at subtelomeric genes and at non-induced promoters of DNA replication genes. Remarkably, the loss of Gcn5 in TORC2 mutant cells restores gene silencing as well as transcriptional induction in response to DNA replication stress. Loss of Bdf2 alleviates excess of Gcn5 binding in TORC2 mutant cells and also rescues the aberrant regulation of transcription in these cells. Furthermore, the loss of either SAGA or Bdf2 suppresses the sensitivity of TORC2 mutant cells to a variety of stresses, including DNA replication, DNA damage, temperature and nutrient stresses. We suggest a role of TORC2 in transcriptional regulation that is critical for gene silencing and gene induction in response to stress and involves the binding of Gcn5 to the chromatin.
Utilization of deep learning to quantify fluid volume of neovascular age-related macular degeneration patients based on swept-source OCT imaging: The ONTARIO study
Authors: Sodhi Simrat K. , Pereira Austin , Oakley Jonathan D. , Golding John , Trimboli Carmelina , Russakoff Daniel B. , Choudhry Netan
Published: February 2022

Purpose

To evaluate the predictive ability of a deep learning-based algorithm to determine long-term best-corrected distance visual acuity (BCVA) outcomes in neovascular age-related macular degeneration (nARMD) patients using baseline swept-source optical coherence tomography (SS-OCT) and OCT-angiography (OCT-A) data.

Methods

In this phase IV, retrospective, proof of concept, single center study, SS-OCT data from 17 previously treated nARMD eyes was used to assess retinal layer thicknesses, as well as quantify intraretinal fluid (IRF), subretinal fluid (SRF), and serous pigment epithelium detachments (PEDs) using a novel deep learning-based, macular fluid segmentation algorithm. Baseline OCT and OCT-A morphological features and fluid measurements were correlated using the Pearson correlation coefficient (PCC) to changes in BCVA from baseline to week 52.

Results

Total retinal fluid (IRF, SRF and PED) volume at baseline had the strongest correlation to improvement in BCVA at month 12 (PCC = 0.652, p = 0.005). Fluid was subsequently sub-categorized into IRF, SRF and PED, with PED volume having the next highest correlation (PCC = 0.648, p = 0.005) to BCVA improvement. Average total retinal thickness in isolation demonstrated poor correlation (PCC = 0.334, p = 0.189). When two features, mean choroidal neovascular membranes (CNVM) size and total fluid volume, were combined and correlated with visual outcomes, the highest correlation increased to PCC = 0.695 (p = 0.002).

Conclusions

In isolation, total fluid volume most closely correlates with change in BCVA values between baseline and week 52. In combination with complimentary information from OCT-A, an improvement in the linear correlation score was observed. Average total retinal thickness provided a lower correlation, and thus provides a lower predictive outcome than alternative metrics assessed. Clinically, a machine-learning approach to analyzing fluid metrics in combination with lesion size may provide an advantage in personalizing therapy and predicting BCVA outcomes at week 52.
Applying citizen science to engage families affected by ovarian cancer in developing genetic service outreach strategies
Authors: McBride Colleen M. , Campbell Gavin P. , Zhao Jingsong , Pentz Rebecca D. , Escoffery Cam , Komonos Michael , Cannova Kelly , Byrne Janice L. B. , Paris Nancy M. , Shepperd James R. , Guan Yue
Published: February 2022

Citizen science (CS) approaches involving non-professional researchers (citizens) as research collaborators has been used infrequently in health promotion generally and specifically, in cancer prevention. Standardized CS approaches may be especially useful for developing communication interventions to encourage families to consider cancer genetic services. We engaged survivors of ovarian cancer and their close relatives as CS collaborators to collect and help interpret data to inform content for a website, printed invitation materials, and short-message reminders. We applied an implementation quality framework, and posed four research questions regarding the feasibility of CS: recruitment, data collection, data quality and evaluation of the experience. CS members were recruited through three networks: clinical sites, local and national cancer support organizations, and online ovarian cancer patient support groups. The professional research team operationalized theory-aligned CS tasks, five data collection options, question banks/scripts for creating surveys, structured interviews, online training and ongoing support from research coaches. 14 CS members agreed to the 12-week and 20-hour commitment for an honorarium. CS members opted to do both qualitative and quantitative assessments. CS members collected 261 surveys and 39 structured interviews. The largest number of surveys were collected for Task 1 (n = 102) to assess survivors’ reactions to different possible options for motivating survivors to visit a study website; 77% of this data were complete (i.e., no missing values). Data collected for tasks 2, 3, 4, and 5 (e.g., assessment of survivors’ and relatives’ respective communication preferences) ranged from 10 to 58 surveys (80% to 84% completeness). All data were collected within the specified time frame. CSs reported 17 hours of work on average and regarded the experience positively. Our experience suggests that CS engagement is feasible, can yield comprehensive quantitative and qualitative data, and is achievable in a relatively a short timeline.
Identifying SARS-COV-2 infected patients through canine olfactive detection on axillary sweat samples; study of observed sensitivities and specificities within a group of trained dogs
Authors: Grandjean Dominique , Gallet Capucine , Julien Clothilde , Sarkis Riad , Muzzin Quentin , Roger Vinciane , Roisse Didier , Dirn Nicolas , Levert Clement , Breton Erwan , Galtat Arnaud , Forget Alexandre , Charreaudeau Sebastien , Gasmi Fabien , Jean-Baptiste Caroline , Petitjean Sebastien , Hamon Katia , Duquesne Jean-Michel , Coudert Chantal , Tourtier Jean-Pierre , Billy Christophe , Wurtz Jean-Marc , Chauvin Anthony , Eyer Xavier , Ziani Sabrina , Prevel Laura , Cherubini Ilaria , Khelili-Houas Enfel , Hausfater Pierre , Devillier Philippe , Desquilbet Loic
Published: February 2022

There is an increasing need for rapid, reliable, non-invasive, and inexpensive mass testing methods as the global COVID-19 pandemic continues. Detection dogs could be a possible solution to identify individuals infected with SARS-CoV-2. Previous studies have shown that dogs can detect SARS-CoV-2 on sweat samples. This study aims to establish the dogs’ sensitivity (true positive rate) which measures the proportion of people with COVID-19 that are correctly identified, and specificity (true negative rate) which measures the proportion of people without COVID-19 that are correctly identified. Seven search and rescue dogs were tested using a total of 218 axillary sweat samples (62 positive and 156 negative) in olfaction cones following a randomised and double-blind protocol. Sensitivity ranged from 87% to 94%, and specificity ranged from 78% to 92%, with four dogs over 90%. These results were used to calculate the positive predictive value and negative predictive value for each dog for different infection probabilities (how likely it is for an individual to be SARS-CoV-2 positive), ranging from 10–50%. These results were compared with a reference diagnostic tool which has 95% specificity and sensitivity. Negative predictive values for six dogs ranged from ≥98% at 10% infection probability to ≥88% at 50% infection probability compared with the reference tool which ranged from 99% to 95%. Positive predictive values ranged from ≥40% at 10% infection probability to ≥80% at 50% infection probability compared with the reference tool which ranged from 68% to 95%. This study confirms previous results, suggesting that dogs could play an important role in mass-testing situations. Future challenges include optimal training methods and standardisation for large numbers of detection dogs and infrastructure supporting their deployment.
Near infrared spectroscopic evaluation of biochemical and crimp properties of knee joint ligaments and patellar tendon
Authors: Torniainen Jari , Ristaniemi Aapo , Sarin Jaakko K. , Prakash Mithilesh , Afara Isaac O. , Finnilä Mikko A. J. , Stenroth Lauri , Korhonen Rami K. , Töyräs Juha
Published: February 2022

Knee ligaments and tendons play an important role in stabilizing and controlling the motions of the knee. Injuries to the ligaments can lead to abnormal mechanical loading of the other supporting tissues (e.g., cartilage and meniscus) and even osteoarthritis. While the condition of knee ligaments can be examined during arthroscopic repair procedures, the arthroscopic evaluation suffers from subjectivity and poor repeatability. Near infrared spectroscopy (NIRS) is capable of non-destructively quantifying the composition and structure of collagen-rich connective tissues, such as articular cartilage and meniscus. Despite the similarities, NIRS-based evaluation of ligament composition has not been previously attempted. In this study, ligaments and patellar tendon of ten bovine stifle joints were measured with NIRS, followed by chemical and histological reference analysis. The relationship between the reference properties of the tissue and NIR spectra was investigated using partial least squares regression. NIRS was found to be sensitive towards the water (R2CV= .65) and collagen (R2CV= .57) contents, while elastin, proteoglycans, and the internal crimp structure remained undetectable. As collagen largely determines the mechanical response of ligaments, we conclude that NIRS demonstrates potential for quantitative evaluation of knee ligaments.
Potential plasma biomarkers: miRNA-29c, miRNA-21, and miRNA-155 in clinical progression of Hepatocellular Carcinoma patients
Authors: Ratnasari Neneng , Lestari Puji , Renovaldi Dede , Raditya Ningsih Juwita , Qoriansas Nanda , Wardana Tirta , Hakim Suharno , Signa Aini Gumilas Nur , Indrarti Fahmi , Triwikatmani Catharina , Bayupurnama Putut , Setyo Heriyanto Didik , Astuti Indwiani , Mubarika Harjana Sofia
Published: February 2022

This study evaluated differences in the clinical appearance of patients with hepatocellular carcinoma (HCC) based on plasma level and regulation of microRNAs (miRNA-29c, miRNA-21, and miRNA-155). The observational-analytical study with a cross-sectional design was conducted on 36 HCC patients and 36 healthy controls. The blood samples were collected from 2 Province Hospitals (Dr. Sardjito Hospital and Prof. Dr. Margono Soekarjo Hospital) for HCC and the Blood Bank Donor of the Indonesian Red Cross for 36 healthy controls. These blood samples were treated as follows: plasma isolation, RNA isolation, cDNA synthesis, quantification by qRT-PCR using a sequence-specific forward primer, and normalization of miRNA using housekeeping-stably miRNA-16. There were only 27 HCC patients with complete clinical variables (neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), platelet count, albumin, C-reactive protein (CRP), and cholinesterase (ChE)) that were able to analyses for regulation miRNAs based on its fold change expression miRNA target. All 27 HCC subjects were follow-up until 3-years of monitoring for their overall survival. The miRNA plasma expression was analyzed by Bio-Rad CFX 96 Manager software to determine the cycle of quantification, followed by the calculation of expression levels using Livak’s methods. Data were analyzed using STATA 11.0, with a significant value of p<0.05. The miRNAs expression of HCC subjects were lower than that healthy control subjects in miRNA-29c (down-regulation 1.83-fold), higher than that healthy control subjects in miRNA 21 and miRNA-155 (up-regulation, 1.74-fold; 1.55-fold) respectively. NLR, CRP, ChE, and platelet count showed a significant difference in miRNA-29c regulation, though neutrophil count showed a significant difference in miRNA-21 and miRNA-155 regulation (p<0.05). Conclusion: Plasma biomarkers: miRNA-21 and miRNA-155 might be potential biomarkers as onco-miR in HCC subjects, while miRNA-29c might act as a tumor suppressor. Significant evidence was identified with clinical progression based on the regulation of miRNAs, which was consistent with miRNA -29c.
Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains
Authors: Joshi Ishita , Peng Jie , Alvino Gina , Kwan Elizabeth , Feng Wenyi
Published: February 2022

We performed a comparative analysis of replication origin activation by genome-wide single-stranded DNA mapping in two yeast strains challenged by hydroxyurea, an inhibitor of the ribonucleotide reductase. We gained understanding of the impact on origin activation by three factors: S-phase checkpoint control, DNA sequence polymorphisms, and relative positioning of origin and transcription unit. Wild type W303 showed a significant reduction of fork progression accompanied by an elevated level of Rad53 phosphorylation as well as physical presence at origins compared to A364a. Moreover, a rad53K227A mutant in W303 activated more origins, accompanied by global reduction of ssDNA across all origins, compared to A364a. Sequence polymorphism in the consensus motifs of origins plays a minor role in determining strain-specific activity. Finally, we identified a new class of origins only active in checkpoint-proficient cells, which we named “Rad53-dependent origins”. Our study presents a comprehensive list of differentially used origins and provide new insights into the mechanisms of origin activation.
Modelling transitions between egalitarian, dynamic leader and absolutist power structures
Authors: Bryden John , Silverman Eric , Powers Simon T.
Published: February 2022

Human groups show a variety of leadership dynamics ranging from egalitarian groups with no leader, to groups with changing leaders, to absolutist groups with a single long-term leader. Here, we model transitions between these different phases of leadership dynamics, investigating the role of inequalities in relationships between individuals. Our results demonstrate a novel riches-to-rags class of leadership dynamics where a leader can be replaced by a new individual. We note that the transition between the three different phases of leadership dynamics resembles transitions in leadership dynamics during the Neolithic period of human history. We argue how technological developments, such as food storage and/or weapons which allow one individual to control large quantities of resources, would mean that relationships became more unequal. In general terms, we provide a model of how individual relationships can affect leadership dynamics and structures.