bluuebunny/crossref_metadata_2025_split huggingface dataset:
SRDFM: Siamese Response Deep Factorization Machine to improve anti-cancer drug recommendation
Authors: Su Ran , Huang YiXuan , Zhang De-gan , Xiao Guobao , Wei Leyi 
Published: December 2021

Abstract
Predicting the response of cancer patients to a particular treatment is a major goal of modern oncology and an important step toward personalized treatment. In the practical clinics, the clinicians prefer to obtain the most-suited drugs for a particular patient instead of knowing the exact values of drug sensitivity. Instead of predicting the exact value of drug response, we proposed a deep learning-based method, named Siamese Response Deep Factorization Machines (SRDFM) Network, for personalized anti-cancer drug recommendation, which directly ranks the drugs and provides the most effective drugs. A Siamese network (SN), a type of deep learning network that is composed of identical subnetworks that share the same architecture, parameters and weights, was used to measure the relative position (RP) between drugs for each cell line. Through minimizing the difference between the real RP and the predicted RP, an optimal SN model was established to provide the rank for all the candidate drugs. Specifically, the subnetwork in each side of the SN consists of a feature generation level and a predictor construction level. On the feature generation level, both drug property and gene expression, were adopted to build a concatenated feature vector, which even enables the recommendation for newly designed drugs with only chemical property known. Particularly, we developed a response unit here to generate weighted genetic feature vector to simulate the biological interaction mechanism between a specific drug and the genes. For the predictor construction level, we built this level integrating a factorization machine (FM) component with a deep neural network component. The FM can well handle the discrete chemical information and both low-order and high-order feature interactions could be sufficiently learned. Impressively, the SRDFM works well on both single-drug recommendation and synergic drug combination. Experiment result on both single-drug and synergetic drug data sets have shown the efficiency of the SRDFM. The Python implementation for the proposed SRDFM is available at at https://github.com/RanSuLab/SRDFM Contact: ran.su@tju.edu.cn, gbx@mju.edu.cn and weileyi@sdu.edu.cn.
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario
Authors: Pellegrino Roberto Maria , Giulietti Matteo , Alabed Husam B R , Buratta Sandra , Urbanelli Lorena , Piva Francesco , Emiliani Carla 
Published: December 2021

Abstract

Summary
LC/MS-based analysis techniques combined with specialized lipid tool allow for the qualitative and quantitative determination of thousands of lipid molecules. Some recent bioinformatics tools have been developed to study changes in the lipid profile in case–control experiments and correlate these changes to different enzyme activity or gene expression. However, the existing tools have the limitation to treat only the assembled lipid molecules. In reality, each individual molecule can be considered as an assembly of smaller parts, often called building blocks. These are the result of a myriad of biochemical synthesis and transformation processes that, from a systems biology perspective, should not be ignored. Here, we present LipidOne, a new lipidomic tool which highlights all qualitative and quantitative changes in lipid building blocks both among all detected lipid classes and among experimental groups. Thanks to LipidOne, even differences in lipid building blocks can now be linked to the activity of specific classes of enzymes, transcripts and genes.

Availability and implementation
LipidOne software is freely available at www.dcbb.unipg.it/LipidOne and https://github.com/matteogiulietti/LipidOne.

Contact
roberto.pellegrino@unipg.it

Supplementary information
Supplementary data are available at Bioinformatics online.
Computed tomography assessment of saw-tooth cardiomyopathy: a case series
Authors: Berarducci Joaquin , Armenta-Moreno Javier Ivan , Espinola-Zavaleta Nilda , Cano-Zarate Roberto , Gutiérrez-Solana-Ossa Ana-Valentina , Keirns Candace 
Published: December 2021

Abstract

Background
Saw-tooth cardiomyopathy (STC) is an unusual type of left ventricular dysplasia. To our knowledge, six cases have been reported in the literature. Two new cases are presented with a review of all the case reports that have been published.

Case summary
Two patients with STC were examined. The first one was a 69-year-old woman with shortness of breath on mild exertion and chest pain, and the second was a 49-year-old man with a history of myocardial infarction who required stent implantation and is now asymptomatic. Both patients revealed findings of STC in the cardiac computed tomography (CT).

Discussion
When analysing the cases and comparing them to the ones reported in the literature; STC is a generally benign heart disease, although the clinical spectrum can range from asymptomatic to heart failure. Imaging studies such as cardiac magnetic resonance and cardiac CT are essential for the diagnosis.
Radiofrequency ablation to achieve durable pulmonary vein isolation
Authors: Mulder Mark J , Kemme Michiel J B , Allaart Cornelis P 
Published: December 2021

AbstractPulmonary vein isolation (PVI) by radiofrequency (RF) ablation is an important alternative to antiarrhythmic drugs in the treatment of symptomatic atrial fibrillation. However, the inability to consistently achieve durable isolation of the pulmonary veins hampers the long-term efficacy of PVI procedures. The large number of factors involved in RF lesion formation and the complex interplay of these factors complicate reliable creation of durable and transmural ablation lesions. Various surrogate markers of ablation lesion formation have been proposed that may provide information on RF lesion completeness. Real-time assessment of these surrogates may aid in the creation of transmural ablation lesions, and therefore, holds potential to decrease the risk of PV reconnection and consequent post-PVI arrhythmia recurrence. Moreover, titration of energy delivery until lesions is transmural may prevent unnecessary ablation and subsequent adverse events. Whereas several surrogate markers of ablation lesion formation have been described over the past decades, a ‘gold standard’ is currently lacking. This review provides a state-of-the-art overview of ablation strategies that aim to enhance durability of RF-PVI, with special focus on real-time available surrogates of RF lesion formation in light of the biophysical basis of RF ablation.
Patterns of Caregiving Among Older Adults With and Without Dementia: A Latent Class Analysis
Authors: Ali Talha , McAvay Gail J , Monin Joan K , Gill Thomas M 
Published: December 2021

Abstract

Objectives
We identify common patterns of caregiving or “care types” among older adults with and without dementia. Prior research has focused on primary caregivers and on the independent effects of individual caregiving attributes. We examine multiple caregivers of older adults, including the primary caregiver, and how multiple caregiving attributes co-occur to shape caregiving types.

Methods
We link 2015 care recipient (N = 1,423) and unpaid caregiver data (N = 2,146) from the National Health and Aging Trends Study and the National Study of Caregiving. Latent class analysis of caregiving attributes, representing care intensity and regularity, and various care activities, was used to construct care types. Multinomial logistic regression was used to examine if the recipients’ dementia status and caregivers’ background characteristics predicted membership in care types.

Results
Five distinguishable care types were identified. Caregivers who were female, adult children, or coresidents, those caring for persons with dementia, and those who had paid help had higher odds of being in the more demanding care types. Conversely, older, White caregivers and those with support for their caregiving activities were less likely to be in a demanding care type.

Discussion
Care types can help us understand sources of heterogeneity in caregiving and effectively target caregiver support services and interventions.
Considerations of sex and gender dimensions by research ethics committees: a scoping review
Authors: Saxena Abha , Lasher Emily , Somerville Claire , Heidari Shirin 
Published: December 2021

Abstract
Despite a growing consensus on the importance of integrating sex and gender in health research, research across disciplines continues to be conducted and reported without a gender focus. Research ethics committees (RECs) can play a particularly powerful role in identifying the gender gaps at an early stage of the development of research protocols. Their role is missing in the dialogue related to improving gender awareness and analysis in health research. A scoping review was conducted to examine the extent to which RECs discuss and consider the inclusion and analysis of sex and gender in health research and to examine the literature regarding the gender balance of RECs. The limited literature around gender and research ethics reveals the power and potential of RECs to ensure that gender dimensions are thoughtfully included in health research, and sheds light on the gaps that exist. These include an under-representation of women on RECs, a lack of awareness of the importance of gender-related aspects in health research and a paucity of gender-related training to RECs. Guidelines such as the Sex and Gender Equity in Research guidelines are required for RECs to strengthen the ways in which health research is gendered from conception of a research protocol to its publication.
High Rickettsial Diversity in Rodents and Their Ectoparasites From the Central Highlands of Madagascar
Authors: Rasoamalala Fanohinjanaharinirina , Parany Mamionah N J , Rahajandraibe Soloandry , Rakotomanga Malala N , Ramihangihajason Tojo , Soarimalala Voahangy , Boyer Sébastien , Rajerison Minoarisoa , Ramasindrazana Beza 
Published: December 2021

Abstract
Rickettsioses are among emerging infectious diseases around the world. In Madagascar, little information is available regarding Rickettsia (Rickettsiales: Rickettsiaceae) diversity and their potential impacts on public health. In fact, molecular screening of ectoparasites of mammals reported the presence of three species, Rickettsia africae, Rickettsia typhi, and Rickettsia felis. The present study aims to investigate the diversity of Rickettsia in small mammals and associated ectoparasites (fleas and ticks) using a molecular approach. In September and December 2016, fieldworks were undertaken in two districts of Madagascar to capture small mammals using standard traps (Tomahawk and Sherman traps) and collect associated ectoparasites. In total, 12 taxa of ectoparasites (5 flea and 7 tick species) were collected from 89 individuals of four species of terrestrial small mammals. Rickettsia spp. were molecularly identified in one specimen of Rattus rattus (Rodentia: Muridae), one specimen of Pulex irritans (Siphonaptera: Pulicidae) as well as four specimens of Ixodes cf. colasbelcouri (Ixodida: Ixodidae). This study showed the presence of three phylogenetically distinct taxa of Rickettsia in small mammals and their ectoparasites. The current study broadens our knowledge on the diversity of Rickettsia in the Central Highlands of Madagascar and highlights for the first time the presence of Ri. felis in R. rattus and in tick, I. cf. colasbelcouri in Madagascar. Additional studies are needed to have exhaustive information on Rickettsia in small mammals and their ectoparasites, to determine their pathogenicity as well as their potential effects on public health in order to update the national policy for the control of emerging infectious diseases in Madagascar.
Assessing Durability and Safety of Permethrin Impregnated Uniforms Used by Outdoor Workers to Prevent Tick Bites after One Year of Use
Authors: Richards Stephanie L , Driver Jeffrey , Dyer Megan C , Mather Thomas N , Funkhouser Sheana , Mitchell Cedar , Anne Balanay Jo , White Avian , Meshnick Steven 
Published: December 2021

Abstract
Long lasting permethrin-impregnated (LLPI) clothing can retain permethrin and repel ticks for up to three months and without exceeding EPA-approved safe levels; however, little is known about longer term effects of wearing LLPI clothing. Here, permethrin content was measured in new forester pants soon after initial impregnation (Insect Shield) and again one year later after being repeatedly worn by foresters in the field. Urine samples were collected from foresters for biomonitoring of permethrin metabolites at multiple time intervals (pre-use, one-month, three-to-four-months, and one-year post-use). Lethality against nymphal Ixodes scapularis Say was measured in clothing after one year of wear by foresters. Furthermore, to test potential variability in permethrin impregnation of different batches of clothing, separate sets of clothing were anonymously sent to Insect Shield for permethrin treatment over a period of three months and permethrin was quantified. Results demonstrated 33% of participants’ pants had no measurable permethrin after one year of wear and permethrin content and tick mortality varied significantly between clothing. Only two of the participants’ clothing resulted in ≥ 30% tick mortality after one year of wear. Significant differences were observed in 3-PBA and trans-DCCA, but not cis-DCCA metabolites in participants over the four measured time points and were higher than general United States population levels. This study provides practical information on the safety (measured by urinary metabolites) over time of LLPI clothing. It also provides snapshots (pre-washing and after one year of wear) of effectiveness of LLPI clothing as personal protective equipment against ticks for outdoor workers.
GammaTile® brachytherapy in the treatment of recurrent glioblastomas
Authors: Gessler Dominic J , Neil Elizabeth C , Shah Rena , Levine Joseph , Shanks James , Wilke Christopher , Reynolds Margaret , Zhang Shunqing , Özütemiz Can , Gencturk Mehmet , Folkertsma Mark , Bell W Robert , Chen Liam , Ferreira Clara , Dusenbery Kathryn , Chen Clark C 
Published: December 2021

AbstractBackgroundGammaTile® (GT) is a recent U.S. Food and Drug Administration (FDA) cleared brachytherapy platform. Here, we report clinical outcomes for recurrent glioblastoma patients after GT treatment following maximal safe resection.MethodsWe prospectively followed twenty-two consecutive Isocitrate Dehydrogenase (IDH) wild-type glioblastoma patients (6 O6-Methylguanine-DNA methyltransferase methylated (MGMTm); sixteen MGMT unmethylated (MGMTu)) who underwent maximal safe resection of recurrent tumor followed by GT placement.ResultsThe cohort consisted of 14 second and eight third recurrences. In terms of procedural safety, there was one 30-day re-admission (4.5%) for an incisional cerebrospinal fluid leak, which resolved with lumbar drainage. No other wound complications were observed. Six patients (27.2%) declined in Karnofsky Performance Score (KPS) after surgery due to worsening existing deficits. One patient suffered a new-onset seizure postsurgery (4.5%). There was one (4.5%) 30-day mortality from intracranial hemorrhage secondary to heparinization for an ischemic limb. The mean follow-up was 733 days (range 279–1775) from the time of initial diagnosis. Six-month local control (LC6) and twelve-month local control (LC12) were 86 and 81%, respectively. Median progression-free survival (PFS) was comparable for MGMTu and MGMTm patients (~8.0 months). Median overall survival (OS) was 20.0 months for the MGMTu patients and 37.4 months for MGMTm patients. These outcomes compared favorably to data in the published literature and an independent glioblastoma cohort of comparable patients without GT treatment.ConclusionsThis clinical experience supports GT brachytherapy as a treatment option in a multi-modality treatment strategy for recurrent glioblastomas.
Osimertinib in advanced EGFR-mutant lung adenocarcinoma with asymptomatic brain metastases: an open-label, 3-arm, phase II pilot study
Authors: Peled Nir , Kian Waleed , Inbar Edna , Goldstein Iris M , Zemel Melanie , Rotem Ofer , Rozenblum Anna B , Nechushtan Hovav , Dudnik Elizabeth , Levin Daniel , Zer Alona , Keren-Rosenberg Shoshana , Yust-Katz Shlomit , Fuchs Vered , Remilah Areen A , Shelef Ilan , Roisman Laila C 
Published: December 2021

Abstract

Background
Osimertinib is selective for both epidermal growth factor receptor (EGFR)-tyrosine-kinase inhibitor (TKI) sensitizing and Thr790Met mutations. While intracranial activity of osimertinib is documented in larger trials, a prospective study focusing exclusively on patients with asymptomatic brain metastases has not been reported.

Methods
In this nonrandomized, phase II, open-label, 3-arm prospective proof-of-concept pilot study, 48 patients with metastatic EGFR-mutant lung adenocarcinoma (LUAD) received osimertinib 80 mg daily. Patients were either treatment naive (arm A = 20) or previously treated with an EGFR-TKI and Thr790Met positive (arm B = 18) or negative (arm C = 10). In cases of isolated intracranial progression, osimertinib dose was escalated (160 mg). The primary endpoints were intracranial objective response rate (iORR) and intracranial disease control rate (iDCR). The secondary endpoint was intracranial progression-free survival (iPFS). This study is registered at Clinicaltrials.gov, NCT02736513.

Results
The iORRs were 84.2%, 66.7%, and 50% and the iDCRs were 94.7%, 94.4%, and 80% in arms A, B, and C, respectively. The median iPFS was 11.8 months (95% CI 7.7 to NA), 7.6 months (95% CI 5.3 to NA), and 6.3 months (95% CI 3.9 to NA) in arms A, B, and C, respectively. Following dose escalation, pooled iORR was 54% (arm A = 5, arm B = 4, arm C = 2). Adverse events were similar to those in previously published literature.

Conclusion
Osimertinib demonstrated high efficacy on brain metastases. All trial arms displayed a significant decrease in the number and diameter of target lesions. These findings indicate that osimertinib is effective for Thr790Met-positive and -negative LUAD patients with asymptomatic brain metastases. Therefore, osimertinib should be considered a viable option for EGFR-mutant patients with brain involvement regardless of their Thr790Met mutation status.
L’évaluation et la prise en charge de la paralysie néonatale du plexus brachial
Authors: Shah Vibhuti , Coroneos Christopher J , Ng Eugene 
Published: December 2021

Résumé
La paralysie néonatale du plexus brachial, qui se manifeste à la naissance, peut être débilitante et avoir des conséquences prolongées. La présentation à la naissance dépend de l’importance de la lésion nerveuse et peut varier entre une faiblesse transitoire et une parésie globale qui touche l’amplitude active des mouvements. Il est essentiel de procéder à des examens cliniques sériels après la naissance et pendant la période néonatale (jusqu’à l’âge d’un mois) pour évaluer le rétablissement et prédire le pronostic à long terme. Le présent document de principes décrit l’évaluation des facteurs de risque des nouveau-nés à la naissance, l’orientation précoce vers une équipe multidisciplinaire spécialisée et les communications entre les intervenants communautaires et les spécialistes pour optimiser le pronostic pendant l’enfance.
Detectable electric current induced by the dark matter axion in a conductor
Authors: Iwazaki Aiichi 
Published: December 2021

Abstract
We propose a method of detecting the dark matter axion by using two slabs of a conductor. The flat surfaces are set face to face, parallel to each other. An external magnetic field B parallel to the surfaces is applied. Radiation converted from the axion arises between the two slabs. When we tune the spacing l between the two surfaces such that l = π/ma with axion mass ma, a resonance occurs so that the radiation becomes strong. Furthermore, the electric current flowing on the surface of the slabs is enhanced. We show that the electric current is large enough to be detectable at the resonance. It reaches 0.7 × 10−9 A $(10^{-5}\, \mbox{eV}/m_a)^{1/2} \, (B/5\, \mbox{T}) \, (L/10\, \mbox{cm}) \, (\sigma /3.3\times 10^7 \, \rm eV)$ using 6N copper for the square slabs with side length L and high electrical conductivity σ at temperature T ∼ 1 K. The power of the Joule heating is $0.3\times 10^{-22} \, \mbox{W} \, (B/5 \, \mbox{T})^2 \, (10^{-5} \, \mbox{eV}/m_a)^{1/2} \, (L/10 \, \mbox{cm})^2 \, (\sigma /3.3\times 10^7 \, \rm eV)$. When we amplify the power using an LC circuit with factor QLC, the signal-to-noise ratio is $4.5\times 10^{4} \, (Q_\mathrm{LC}/10^6) \, (B/5 \, \mbox{T})^2 \, (t_\mathrm{obs}/1\, \mathrm{s})^{1/2}\, (10^{-5} \, \mbox{eV}/m_a) \, (L/10 \, \mbox{cm})^2 \, (\sigma /3.3\times 10^7 \, \rm eV)$ with an observation time of tobs.
Outcomes of a Two-Visit Protocol for Long Acting Reversible Contraception for Adolescents and Young Adults
Authors: Wilkinson Tracey A. , Edmonds Brownsyne Tucker , Cheng Erika R. 
Published: December 2021

(Abstracted from Contraception 2021; doi:10.1016/j.contraception.2021.07.107)
Given their effectiveness, intrauterine devices (IUDs) and contraceptive arm implants are recommended for first-line contraception in nulliparous women by the American Academy of Pediatrics and the American College of Obstetrics and Gynecology. Same-day contraceptive placement is often unavailable for nonmedical reasons, despite evidence that it increases uptake and utilization resulting in significant reduction in unintended pregnancy, abortion, and Medicaid costs.
A Novel Algorithm With Paired Predictive Indexes to Stratify the Risk Levels of Neonates With Invasive Bacterial Infections: A Multicenter Cohort Study
Authors: Yin Zhanghua , Chen Yan , Zhong Wenhua , Shan Liqin , Zhang Qian , Gong Xiaohui , Li Jing , Lei Xiaoping , Zhou Qin , Zhao Youyan , Chen Chao , Zhang Yongjun 
Published: December 2021

Background:
Our aim was to develop a predictive model comprising clinical and laboratory parameters for early identification of full-term neonates with different risks of invasive bacterial infections (IBIs).

Methods:
We conducted a retrospective study including 1053 neonates presenting in 9 tertiary hospitals in China from January 2010 to August 2019. An algorithm with paired predictive indexes (PPIs) for risk stratification of neonatal IBIs was developed. Predictive performance was validated using k-fold cross-validation.

Results:
Overall, 166 neonates were diagnosed with IBIs (15.8%). White blood cell count, C-reactive protein level, procalcitonin level, neutrophil percentage, age at admission, neurologic signs, and ill-appearances showed independent associations with IBIs from stepwise regression analysis and combined into 23 PPIs. Using 10-fold cross-validation, a combination of 7 PPIs with the highest predictive performance was picked out to construct an algorithm. Finally, 58.1% (612/1053) patients were classified as low-risk cases. The sensitivity and negative predictive value of the algorithm were 95.3% (95% confidence interval: 91.7−98.3) and 98.7% (95% confidence interval: 97.8−99.6), respectively. An online calculator based on this algorithm was developed for clinical use.

Conclusions:
The new algorithm constructed for this study was a valuable tool to screen neonates with suspected infection. It stratified risk levels of IBIs and had an excellent predictive performance.