bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creation of optical chains with prescribed characteristics
Authors: Zeng Yongxi , Yu Yanzhong , Zhan Qiwen 
Published: February 2023

Abstract
We report a non-iterative method to create an arbitrarily spatially-orientated optical chain with prescribed characteristics through the use of antenna radiation theory and time reversal methodology. A pair of antennas consisting of an electric current line source (ELS) and a magnetic current line source (MLS) are employed to yield the required incident field pattern for

4
π

focusing system. Numerical results demonstrate that the direction of the generated optical chain is consistent with the orientation of the combined antennas, and the length of the optical chain is approximately equal to the length of the combined antennas, and the amount, position and spacing of the dark hollow spots are determined by the length of the combined antenna and the amplitude periodic coefficient of the ELS. The generated optical chains may find potential applications in multi-points optical capture and particle delivery along prescribed directions.
Image-plane coherent diffractive imaging using variable-ratio lateral-shearing interferometry
Authors: Zhou Mengyu , Zhang Xiuping , Zhang Junyong , Zhu Jianqiang 
Published: February 2023

Abstract
Coherent diffractive imaging (CDI) is an imaging technique that directly recovers the amplitude and phase information of the test object from the recorded diffraction patterns with an iterative algorithm. Different from the traditional CDI, here an image-plane CDI is proposed based on the variable-ratio lateral-shearing interferometry. Variable-ratio operation can realize three optical functions, the first is the array imaging, the second is the image relay, and the third is variable-ratio shear. In experiment, a frame of

2
×
2

array diffraction patterns is recorded in one single exposure. Then, each sub-diffraction pattern is extracted through the image features and is sequentially used to recover the test object by phase retrieval. The experimental results of phase-only and amplitude-only object verify the effectiveness and robustness of our proposed method. This method not only circumvents the calibration problem of gratings but also strengthens the convergence conditions required for phase retrieval, which has broad applications in fields such as optical imaging and wavefront sensing.
Recent advances in hole-spin qubits
Authors: Fang Yinan , Philippopoulos Pericles , Culcer Dimitrie , Coish W A , Chesi Stefano 
Published: February 2023

Abstract
In recent years, hole-spin qubits based on semiconductor quantum dots have advanced at a rapid pace. We first review the main potential advantages of these hole-spin qubits with respect to their electron-spin counterparts and give a general theoretical framework describing them. The basic features of spin–orbit coupling and hyperfine interaction in the valence band are discussed, together with consequences on coherence and spin manipulation. In the second part of the article, we provide a survey of experimental realizations, which spans a relatively broad spectrum of devices based on GaAs, Si and Si/Ge heterostructures. We conclude with a brief outlook.
The Management of Lumps, Bumps, and Contour Irregularities of the Lower Eyelid and Cheek After Poor Outcome Fat Transfer
Authors: Ugradar Shoaib , Wang Yao , Patel Amy , Holds John B , Douglas Raymond , Massry Guy 
Published: February 2023

Abstract

Background
The increasing popularity of fat transfer (FT) to the lower eyelids has led to an increase in unwanted lumps, bumps, and contour irregularities (LBCs). Few studies have addressed the management of LBCs.

Objectives
The aim of this study was to address the management of LBCs.

Methods
In this retrospective review, charts of all patients presenting for evaluation of LBCs following FT procedures to the lower eyelid were reviewed. Clinical characteristics on presentation and surgical findings were evaluated. Patient postoperative clinical course and complications were also documented.

Results
Forty-eight patients were included (45 women and 3 men), with an average follow-up of 14 months (range, 5-24 months). In 65%, LBCs manifested above the lower orbital rim (AR) and in 35% they were noted AR and below the rim (AR/BR). The type of contour deficits noted were a solitary nodule (SN) in 54%, a mixed picture (MP) in 23%, diffuse enlargement (DE) in 17%, and multiple nodules (MNs) in 6%. Combining lesion location and type of contour deficit, the most common presentation was an SN-AR in 22 patients (46%), followed by an MP-AR/BR in 8 patients (17%), and a DE-AR/BR in 5 patients (10%). Surgical findings revealed that grafted fat is consistently found separate from native eyelid/orbital fat, and within the orbicularis muscle when AR, and within the orbicularis muscle or the deep suborbicularis oculi fat when BR.

Conclusions
LBCs tend to manifest in characteristic patterns with a predilection for an AR location. Recommendations on the diagnosis and management of these lesions are provided.
An experimental field test of female defense in territorial male collared lizards
Authors: Baird Troy A , Leibold Dalton C 
Published: February 2023

AbstractA widely held principle in behavioral ecological research is that polygynous social systems evolve either by direct male defense of females or male defense of resources, although which of these mechanisms applies in particular species is rarely examined experimentally. We tested the relative importance of female versus resource defense in polygynous territorial male collared lizards (Crotaphytus collaris). Using a novel experimental design, we temporarily removed some of the resident females from male territories to create a female-free removal zone, whereas resident females were left intact within a non-removal zone. We then compared activity of males within each zone during three experimental phases; before we removed females, for two days when females were absent, and the day after return of females. If males defend females directly, we expected them to adjust the location of their patrol and display within removal and non-removal zones depending on the presence/absence of females, whereas we expected no such change if males defend resources. Male activity in the removal zone generally decreased when females were removed but then increased when females were replaced, whereas we observed the opposite pattern in the non-removal zone. The observed shifts in the location of patrol and display in response to the presence/absence of females, while resources remained constant, indicate that polygynous male collared lizards defend females directly. Our results suggest that male collared lizards take advantage of strong female philopatry to relatively small areas by focusing their patrol and display activities where potential mates reside.
Improving classification of correct and incorrect protein–protein docking models by augmenting the training set
Authors: Barradas-Bautista Didier , Almajed Ali , Oliva Romina , Kalnis Panos , Cavallo Luigi 
Published: February 2023

Abstract

Motivation
Protein–protein interactions drive many relevant biological events, such as infection, replication and recognition. To control or engineer such events, we need to access the molecular details of the interaction provided by experimental 3D structures. However, such experiments take time and are expensive; moreover, the current technology cannot keep up with the high discovery rate of new interactions. Computational modeling, like protein–protein docking, can help to fill this gap by generating docking poses. Protein–protein docking generally consists of two parts, sampling and scoring. The sampling is an exhaustive search of the tridimensional space. The caveat of the sampling is that it generates a large number of incorrect poses, producing a highly unbalanced dataset. This limits the utility of the data to train machine learning classifiers.

Results
Using weak supervision, we developed a data augmentation method that we named hAIkal. Using hAIkal, we increased the labeled training data to train several algorithms. We trained and obtained different classifiers; the best classifier has 81% accuracy and 0.51 Matthews’ correlation coefficient on the test set, surpassing the state-of-the-art scoring functions.

Availability and implementation
Docking models from Benchmark 5 are available at https://doi.org/10.5281/zenodo.4012018. Processed tabular data are available at https://repository.kaust.edu.sa/handle/10754/666961. Google colab is available at https://colab.research.google.com/drive/1vbVrJcQSf6\_C3jOAmZzgQbTpuJ5zC1RP?usp=sharing

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
WMDS.net: a network control framework for identifying key players in transcriptome programs
Authors: Cheng Xiang , Amanullah Md , Liu Weigang , Liu Yi , Pan Xiaoqing , Zhang Honghe , Xu Haiming , Liu Pengyuan , Lu Yan 
Published: February 2023

Abstract

Motivation
Mammalian cells can be transcriptionally reprogramed to other cellular phenotypes. Controllability of such complex transitions in transcriptional networks underlying cellular phenotypes is an inherent biological characteristic. This network controllability can be interpreted by operating a few key regulators to guide the transcriptional program from one state to another. Finding the key regulators in the transcriptional program can provide key insights into the network state transition underlying cellular phenotypes.

Results
To address this challenge, here, we proposed to identify the key regulators in the transcriptional co-expression network as a minimum dominating set (MDS) of driver nodes that can fully control the network state transition. Based on the theory of structural controllability, we developed a weighted MDS network model (WMDS.net) to find the driver nodes of differential gene co-expression networks. The weight of WMDS.net integrates the degree of nodes in the network and the significance of gene co-expression difference between two physiological states into the measurement of node controllability of the transcriptional network. To confirm its validity, we applied WMDS.net to the discovery of cancer driver genes in RNA-seq datasets from The Cancer Genome Atlas. WMDS.net is powerful among various cancer datasets and outperformed the other top-tier tools with a better balance between precision and recall.

Availability and implementation
https://github.com/chaofen123/WMDS.net.

Supplementary information
Supplementary data are available at Bioinformatics online.
Dimethyl-α-cyclodextrin induces capacitation by removing phospholipids from the plasma membrane of mouse sperm
Authors: Nakao Satohiro , Ito Kotono , Sakoh Kazuhito , Takemoto Kenji , Watanabe Hitomi , Kondoh Gen , Irie Tetsumi , Nakagata Naomi , Takeo Toru 
Published: February 2023

AbstractCapacitation is an important event in the completion of fertilization by mammalian sperm. Cholesterol efflux is a trigger of capacitation. In general, cholesterol acceptors of albumin and β-cyclodextrins are used to induce capacitation during in vitro fertilization. Previously, we reported that methyl-β-cyclodextrin (MBCD), which is composed of seven glucoses, had a higher ability to induce capacitation than bovine serum albumin (BSA) in frozen–thawed mouse sperm. Comparison of albumin and cyclodextrins is helpful for understanding the mechanism of capacitation. In this study, we examined the effects of albumin, MBCD, and a different type of cyclodextrin, dimethyl-α-cyclodextrin (DMACD), which is composed of six glucoses, on several events of sperm capacitation. We showed that DMACD induced sperm capacitation and promoted fertilization ability. The time required to increase the fertilization rate differed among BSA, MBCD, and DMACD. BSA and MBCD enhanced cholesterol and phospholipid efflux, whereas DMACD enhanced only phospholipid efflux. BSA, MBCD, and DMACD increased sperm membrane fluidity, rearrangement of the lipid raft, and the acrosome reaction. These findings suggest that phospholipid efflux is a novel trigger of capacitation. Increasing the choice of sperm capacitation inducers may be useful for improving in vitro fertilization (IVF) techniques not only in mice, but also in various species in which it has been difficult to produce embryos by IVF.
Standard follow-up after curative surgery for advanced gastric cancer: secondary analysis of a multicentre randomized clinical trial (KLASS-02)
Authors: Park Sin Hye , Hyung Woo Jin , Yang Han-Kwang , Park Young-Kyu , Lee Hyuk-Joon , An Ji Yeong , Kim Wook , Kim Hyoung-Il , Kim Hyung-Ho , Ryu Seung Wan , Hur Hoon , Kim Min-Chan , Kong Seong-Ho , Cho Gyu Seok , Kim Jin-Jo , Park Do Joong , Kim Young-Woo , Kim Jong Won , Lee Joo-Ho , Han Sang-Uk , Ryu Keun Won 
Published: February 2023

Abstract

Background
The benefit of regular follow-up after curative resection for gastric cancer is controversial as there is no evidence that it will improve survival. This study assessed whether regular follow-up leads to improved survival in patients after surgery for gastric cancer.

Methods
A secondary analysis was undertaken of patients who participated in an RCT of laparoscopic versus open distal gastrectomy for advanced gastric cancer between November 2011 and April 2015. Depending on whether patients were compliant with the initial trial follow-up protocol or not, they were analysed as having had either regular or irregular follow-up. Clinicopathological characteristics, recurrence patterns, detection, treatments, and survival were compared between the groups.

Results
The regular and irregular follow-up groups comprised 712 and 263 patients respectively. Disease recurrence within 36 months was more common in the regular group than in the irregular group (17.0 versus 11.4 per cent; P = 0.041). Recurrence patterns did not differ between the groups. The 3-year recurrence-free survival rate was worse in the regular than in the irregular group (81.2 versus 86.5 per cent; P = 0.031). However, the 5-year overall survival rate was comparable (84.5 versus 87.5 per cent respectively; P = 0.160). Multivariable analysis revealed that type of follow-up was not an independent factor affecting 5-year overall survival.

Conclusion
Regular follow-up after radical gastrectomy was not associated with improved overall survival.
Children and bioethics: clarifying consent and assent in medical and research settings
Authors: Spriggs Merle 
Published: February 2023

AbstractIntroductionThe concept of consent in the pediatric setting is complex and confusing. Clinicians and researchers want to know whose consent they should obtain, when a child can provide independent consent and how that is determined. The aim of this article is to establish what produces the justification to proceed with medical or research interventions involving children and the role of consent in that. I clarify concepts such as consent, assent, capacity and competence.Source of dataLiterature review.Areas of agreementEngaging with children and involving them in decisions about matters that affect them is a good thing.Areas of controversyThe role of competence or capacity and the question of when a child can provide sole consent.Growing pointsFlawed assumptions around competence/capacity.Areas for developing researchAn account of children’s well-being that accommodates children’s interests during the transition to adulthood.
Untangling the Hymenaea stigonocarpa complex (Fabaceae) using population genetics and morphology
Authors: Pinto Rafael Barbosa , Braga Ferreira Ramilla Dos Santos , Rosa Gonçalves Ariany , Telles Mariana Pires De Campos , José Chaves Lázaro , Alves Rezende Andréia , Diniz-Filho José Alexandre Felizola , Mansano Vidal De Freitas 
Published: February 2023

Abstract
Hymenaea is a genus of Fabaceae easily recognized by vegetative characteristics. However, the circumscription of some species has been historically challenging. The tangled circumscription of H. stigonocarpa has been addressed in several molecular and morphological studies, but some of the morphological confusion has yet to be resolved. Thus, in this study we used population genetics coupled with detailed morphological analyses to improve taxonomic definition in this complex, currently comprising two varieties (H. stigonocarpa vars. stigonocarpa and brevipetiolata). Bayesian and population genetic structure analyses were conducted using nine nuclear microsatellite loci for 1034 individuals from 35 populations. The morphometric analyses were performed using leaflet characters. Our results support the existence of five genetically structured clusters, and morphometric analyses support the recognition of two clusters, emphasizing H. stigonocarpa var. brevipetiolata as an exclusive genetic and morphological group, encouraging us to make changes in its taxonomic ranking. Thus, we propose the adoption of specific status for H. stigonocarpa var. brevipetiolata on the basis of its population genetics and morphology. In addition to the population genetics data and morphological analyses, a taxonomic treatment with illustrations is provided.
Subthalamic and nigral neurons are differentially modulated during parkinsonian gait
Authors: Gulberti Alessandro , Wagner Jonas R , Horn Martin A , Reuss Jacob H , Heise Miriam , Koeppen Johannes A , Pinnschmidt Hans O , Westphal Manfred , Engel Andreas K , Gerloff Christian , Sharott Andrew , Hamel Wolfgang , Moll Christian K E , Pötter-Nerger Monika 
Published: February 2023

Abstract
The parkinsonian gait disorder and freezing of gait are therapeutically demanding symptoms with considerable impact on quality of life. The aim of this study was to assess the role of subthalamic and nigral neurons in the parkinsonian gait control using intraoperative microelectrode recordings of basal ganglia neurons during a supine stepping task.
Twelve male patients (56 ± 7 years) suffering from moderate idiopathic Parkinson’s disease (disease duration 10 ± 3 years, Hoehn and Yahr stage 2), undergoing awake neurosurgery for deep brain stimulation, participated in the study. After 10 s resting, stepping at self-paced speed for 35 s was followed by short intervals of stepping in response to random ‘start’ and ‘stop’ cues. Single- and multi-unit activity was analysed offline in relation to different aspects of the stepping task (attentional ‘start’ and ‘stop’ cues, heel strikes, stepping irregularities) in terms of firing frequency, firing pattern and oscillatory activity.
Subthalamic nucleus and substantia nigra neurons responded to different aspects of the stepping task. Of the subthalamic nucleus neurons, 24% exhibited movement-related activity modulation as an increase of the firing rate, suggesting a predominant role of the subthalamic nucleus in motor aspects of the task, while 8% of subthalamic nucleus neurons showed a modulation in response to the attentional cues. In contrast, responsive substantia nigra neurons showed activity changes exclusively associated with attentional aspects of the stepping task (15%). The firing pattern of subthalamic nucleus neurons revealed gait-related firing regularization and a drop of beta oscillations during the stepping performance. During freezing episodes instead, there was a rise of beta oscillatory activity.
This study shows for the first time specific, task-related subthalamic nucleus and substantia nigra single-unit activity changes during gait-like movements in humans with differential roles in motor and attentional control of gait. The emergence of perturbed firing patterns in the subthalamic nucleus indicates a disrupted information transfer within the gait network, resulting in freezing of gait.
Multifaceted nanoparticles: emerging mechanisms and therapies in neurodegenerative diseases
Authors: Mistretta Miriam , Farini Andrea , Torrente Yvan , Villa Chiara 
Published: February 2023

Abstract
Neurodegenerative diseases are a major global health burden particularly with the increasing ageing population. Hereditary predisposition and environmental risk factors contribute to the heterogeneity of existing pathological phenotypes. Traditional clinical interventions focused on the use of small drugs have often led to failures due to the difficulties in crossing the blood–brain barrier and reaching the brain. In this regard, nanosystems can specifically deliver drugs and improve their bioavailability, overcoming some of the major challenges in neurodegenerative disease treatment.
This review focuses on the use of nanosystems as an encouraging therapeutic approach targeting molecular pathways involved in localized and systematic neurodegenerative diseases. Among the latter, Friedreich’s ataxia is an untreatable complex multisystemic disorder and the most widespread type of ataxia; it represents a test case to validate the clinical potential of therapeutic strategies based on nanoparticles with pleiotropic effects.
Integrative miRNA–mRNA profiling of human epidermis: unique signature of SCN9A painful neuropathy
Authors: Andelic Mirna , Salvi Erika , Marcuzzo Stefania , Marchi Margherita , Lombardi Raffaella , Cartelli Daniele , Cazzato Daniele , Mehmeti Elkadia , Gelemanovic Andrea , Paolini Matilde , Pardo Carlotta , D’Amato Ilaria , Hoeijmakers Janneke G J , Dib-Hajj Sulayman , Waxman Stephen G , Faber Catharina G , Lauria Giuseppe 
Published: February 2023

AbstractPersonalized management of neuropathic pain is an unmet clinical need due to heterogeneity of the underlying aetiologies, incompletely understood pathophysiological mechanisms and limited efficacy of existing treatments. Recent studies on microRNA in pain preclinical models have begun to yield insights into pain-related mechanisms, identifying nociception-related species differences and pinpointing potential drug candidates.With the aim of bridging the translational gap towards the clinic, we generated a human pain-related integrative miRNA and mRNA molecular profile of the epidermis, the tissue hosting small nerve fibres, in a deeply phenotyped cohort of patients with sodium channel-related painful neuropathy not responding to currently available therapies.We identified four miRNAs strongly discriminating patients from healthy individuals, confirming their effect on differentially expressed gene targets driving peripheral sensory transduction, transmission, modulation and post-transcriptional modifications, with strong effects on gene targets including NEDD4. We identified a complex epidermal miRNA–mRNA network based on tissue-specific experimental data suggesting a cross-talk between epidermal cells and axons in neuropathy pain. Using immunofluorescence assay and confocal microscopy, we observed that Nav1.7 signal intensity in keratinocytes strongly inversely correlated with NEDD4 expression that was downregulated by miR-30 family, suggesting post-transcriptional fine tuning of pain-related protein expression. Our targeted molecular profiling advances the understanding of specific neuropathic pain fine signatures and may accelerate process towards personalized medicine in patients with neuropathic pain.
Media populism and the metanarrative of God in the Philippines
Authors: Ragragio Jefferson Lyndon D 
Published: February 2023

AbstractThis article uses the concept of media populism to analyze the sophisticated role of networked platforms in organizing political discourses. Building on the scholarship on mediatization and mediated populism, it examines the mediated appeal of the God metanarrative—Religious Duterte, Catholic Church, Apollo Quiboloy, and Daily Prayer—and shows how God-related posts amplify the communicative style of populism in the Philippines. The God metanarrative on Facebook inspires communal engagement much as it polarizes the civil consensus on free expression and inclusive nationalism. The embedding of non-conflictual sentiments in the digital sphere blurs the precarious line between free expression of religious views and of political support, enabling political entrepreneurs to exploit the former as a way to consolidate the latter.