bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical and molecular characterization of 1q43q44 deletion and corpus callosum malformations: 2 new cases and literature review
Authors: Khadija Bochra , Rjiba Khouloud , Dimassi Sarra , Dahleb Wafa , Kammoun Molka , Hannechi Hanen , Miladi Najoua , Gouider-khouja Neziha , Saad Ali , Mougou-Zerelli Soumaya
Published: October 2022

Background

Corpus callosum malformations (CCM) represent one of the most common congenital cerebral malformations with a prevalence of around one for 4000 births. There have been at least 230 reports in the literature concerning 1q43q44 deletions of varying sizes discovered using chromosomal microarrays. This disorder is distinguished by global developmental delay, seizures, hypotonia, corpus callosum defects, and significant craniofacial dysmorphism. In this study, we present a molecular cytogenetic analysis of 2 Tunisian patients with corpus callosum malformations. Patient 1 was a boy of 3 years old who presented psychomotor retardation, microcephaly, behavioral problems, interventricular septal defect, moderate pulmonary stenosis, hypospadias, and total CCA associated with delayed encephalic myelination. Patient 2 was a boy of 9 months. He presented a facial dysmorphia, a psychomotor retardation, an axial hypotonia, a quadri pyramidal syndrome, a micropenis, and HCC associated with decreased volume of the periventricular white matter. Both the array comparative genomic hybridization and fluorescence in situ hybridization techniques were used.

Results

Array CGH analysis reveals that patient 1 had the greater deletion size (11,7 Mb) at 1q43. The same region harbors a 2,7 Mb deletion in patient 2. Here, we notice that the larger the deletion, the more genes are likely to be involved, and the more severe the phenotype is likely to be. In both patients, the commonly deleted region includes six genes: PLD5, AKT3, ZNF238, HNRNPU, SDCCAG8 and CEP170. Based on the role of the ZNF238 gene in neuronal proliferation, migration, and cortex development, we hypothesized that the common deletion of ZNF238 in both patients seems to be the most responsible for corpus callosum malformations. Its absence may directly cause CCM. In addition, due to their high expression in the brain, PLD5 and FMN2 could modulate in the CCM phenotype.

Conclusion

Our findings support and improve the complex genotype–phenotype correlations previously reported in the 1qter microdeletion syndrome and define more precisely the neurodevelopmental phenotypes associated with genetic alterations of several genes related to this pathology.
H3K18 lactylation marks tissue-specific active enhancers
Authors: Galle Eva , Wong Chee-Wai , Ghosh Adhideb , Desgeorges Thibaut , Melrose Kate , Hinte Laura C. , Castellano-Castillo Daniel , Engl Magdalena , de Sousa Joao Agostinho , Ruiz-Ojeda Francisco Javier , De Bock Katrien , Ruiz Jonatan R. , von Meyenn Ferdinand
Published: October 2022

Background

Histone lactylation has been recently described as a novel histone post-translational modification linking cellular metabolism to epigenetic regulation.

Results

Given the expected relevance of this modification and current limited knowledge of its function, we generate genome-wide datasets of H3K18la distribution in various in vitro and in vivo samples, including mouse embryonic stem cells, macrophages, adipocytes, and mouse and human skeletal muscle. We compare them to profiles of well-established histone modifications and gene expression patterns. Supervised and unsupervised bioinformatics analysis shows that global H3K18la distribution resembles H3K27ac, although we also find notable differences. H3K18la marks active CpG island-containing promoters of highly expressed genes across most tissues assessed, including many housekeeping genes, and positively correlates with H3K27ac and H3K4me3 as well as with gene expression. In addition, H3K18la is enriched at active enhancers that lie in proximity to genes that are functionally important for the respective tissue.

Conclusions

Overall, our data suggests that H3K18la is not only a marker for active promoters, but also a mark of tissue specific active enhancers.
Engineering Yarrowia lipolytica for the sustainable production of β-farnesene from waste oil feedstock
Authors: Liu Yinghang , Zhang Jin , Li Qingbin , Wang Zhaoxuan , Cui Zhiyong , Su Tianyuan , Lu Xuemei , Qi Qingsheng , Hou Jin
Published: October 2022

Background

β-Farnesene is a sesquiterpene with versatile industrial applications. The production of β-farnesene from waste lipid feedstock is an attractive method for sustainable production and recycling waste oil. Yarrowia lipolytica is an unconventional oleaginous yeast, which can use lipid feedstock and has great potential to synthesize acetyl-CoA-derived chemicals.

Results

In this study, we engineered Y. lipolytica to produce β-farnesene from lipid feedstock. To direct the flux of acetyl-CoA, which is generated from lipid β-oxidation, to β-farnesene synthesis, the mevalonate synthesis pathway was compartmentalized into peroxisomes. β-Farnesene production was then engineered by the protein engineering of β-farnesene synthase and pathway engineering. The regulation of lipid metabolism by enhancing β-oxidation and eliminating intracellular lipid synthesis was further performed to improve the β-farnesene synthesis. As a result, the final β-farnesene production with bio-engineering reached 35.2 g/L and 31.9 g/L using oleic acid and waste cooking oil, respectively, which are the highest β-farnesene titers reported in Y. lipolytica.

Conclusions

This study demonstrates that engineered Y. lipolytica could realize the sustainable production of value-added acetyl-CoA-derived chemicals from waste lipid feedstock.
Capparis spinosa improves non-alcoholic steatohepatitis through down-regulating SREBP-1c and a PPARα-independent pathway in high-fat diet-fed rats
Authors: Akbari Rasoul , Yaghooti Hamid , Jalali Mohammad Taha , Khorsandi Laya Sadat , Mohammadtaghvaei Narges
Published: October 2022

Objective

Non-alcoholic steatohepatitis (NASH) has become a global medical problem. Currently, there is no approved pharmacologic treatment for this condition. Previous studies have suggested that in the pathogenesis of this disease, regulatory pathways associated with de novo lipogenesis and β-oxidation pathways genes are misregulated. Capparis spinosa (CS) belongs to the family of Capparidaceae and is a traditional plant used to treat various diseases, particularly dyslipidemia. The compounds and extracts of this plant in In vivo and in vitro studies resulted in a reduction in lipid profiles and glucose. However, the mechanism of these effects remains unknown. This study aimed to evaluate the effects of (CS) fruit extract on NASH compared to fenofibrate and explored the related molecular mechanism.

Results

In the rats (n = 40) model of NASH, biochemical and histopathological examinations showed that liver steatosis, inflammation, and hepatic fibrosis were markedly attenuated in response to CS and fenofibrate interventions. At the molecular level, CS treatment down-regulated sterol regulatory element-binding protein-1c (SREBP-1c) (p < 0.001), acetyl-CoA carboxylase (ACC) (p < 0.001), and up-regulated Carnitine palmitoyltransferase I (CPT1) expression (p < 0.001). In conclusion, CS has favorable therapeutic effects for NASH, which was associated with ameliorating steatosis and fibrosis via regulation of the DNL and β-oxidation pathway genes.

Graphical Abstract
Effects of Moringa oleifera on working memory: an experimental study with memory-impaired Wistar rats tested in radial arm maze
Authors: Afrin Sadia , Hossain Ahmed , Begum Shelina
Published: October 2022

Objective

Memory impairment is a serious problem that has a significant negative impact on survival and quality of life. When used for a long time, drugs used to treat memory loss become less effective and have more side effects, making therapy more difficult. Different medicinal plants are now being highlighted because of their valuable applications and low risk of adverse effects. Moringa oleifera is one of these plants that has gained much attention due to its diverse biological functions. The study aimed to determine the effects of Moringa oleifera on working memory in memory-impaired Wistar rats.

Results

For this experimental study, 30 male Wistar rats having 150–250 g bodyweight were divided equally into three groups: Group-I/normal memory group (treated with oral normal saline 5 ml/kg body weight), Group-II/memory-impaired group (induced by intraperitoneal ketamine 15 mg/kg body weight), and Group-III/experimental group (treated with oral Moringa oleifera 200 mg/kg bodyweight and intraperitoneal ketamine 15 mg/kg body weight). The experimental group showed significantly fewer working memory errors than the memory-impaired group. The experimental group also provides the lowest variability of WMEs among groups. Thus, the study concludes that M. oleifera can prevent ketamine-induced memory impairment in Wistar rats.
Enhanced fear limits behavioral flexibility in Shank2-deficient mice
Authors: Yun Miru , Kim Eunjoon , Jung Min Whan
Published: October 2022

Background

A core symptom of autism spectrum disorder (ASD) is repetitive and restrictive patterns of behavior. Cognitive inflexibility has been proposed as a potential basis for these symptoms of ASD. More generally, behavioral inflexibility has been proposed to underlie repetitive and restrictive behavior in ASD. Here, we investigated whether and how behavioral flexibility is compromised in a widely used animal model of ASD.

Methods

We compared the behavioral performance of Shank2-knockout mice and wild-type littermates in reversal learning employing a probabilistic classical trace conditioning paradigm. A conditioned stimulus (odor) was paired with an unconditioned appetitive (water, 6 µl) or aversive (air puff) stimulus in a probabilistic manner. We also compared air puff-induced eye closure responses of Shank2-knockout and wild-type mice.

Results

Male, but not female, Shank2-knockout mice showed impaired reversal learning when the expected outcomes consisted of a water reward and a strong air puff. Moreover, male, but not female, Shank2-knockout mice showed stronger anticipatory eye closure responses to the air puff compared to wild-type littermates, raising the possibility that the impairment might reflect enhanced fear. In support of this contention, male Shank2-knockout mice showed intact reversal learning when the strong air puff was replaced with a mild air puff and when the expected outcomes consisted of only rewards.

Limitations

We examined behavioral flexibility in one behavioral task (reversal learning in a probabilistic classical trace conditioning paradigm) using one ASD mouse model (Shank2-knockout mice). Thus, future work is needed to clarify the extent to which our findings (that enhanced fear limits behavioral flexibility in ASD) can explain the behavioral inflexibility associated with ASD. Also, we examined only the relationship between fear and behavioral flexibility, leaving open the question of whether abnormalities in processes other than fear contribute to behavioral inflexibility in ASD. Finally, the neurobiological mechanisms linking Shank2-knockout and enhanced fear remain to be elucidated.

Conclusions

Our results indicate that enhanced fear suppresses reversal learning in the presence of an intact capability to learn cue-outcome contingency changes in Shank2-knockout mice. Our findings suggest that behavioral flexibility might be seriously limited by abnormal emotional responses in ASD.
Irony detection in patients with borderline personality disorder: an experimental study examining schizotypal traits, response biases and empathy
Authors: Felsenheimer Anne Katrin , Kieckhäfer Carolin , Rapp Alexander Michael
Published: October 2022

Background

In verbal irony we often convey meanings that oppose the literal words. To look behind these words, we need to integrate perspectives of ourselves, others, and their beliefs about us. Although patients with borderline personality disorder (BPD) experience problems in social cognition and schizotypal symptoms, research on irony comprehension mainly focused on the schizophrenic spectrum. Accounting for possible negative biases in BPD, the current study examined the detection of praising and critical irony in a text messaging interface.

Methods

The cross-sectional study included 30 patients and 30 matched controls, who completed measures of cognitive and affective empathy (Interpersonal Reactivity Index, IRI), schizotypal (Schizotypal Personality Questionnaire; SPQ), and borderline symptoms (Borderline Symptom List; BSL-23) and the irony detection task. The irony task contained critical and praising remarks embedded in text messages. Asking for literality (ironic vs. literal) and intention ratings (critical to praising) of the stimuli, it allowed to analyze the sensitivity of literality detection as well as implicit and explicit response biases in a signal detection framework.

Results

Borderline symptoms explained lower sensitivity for the detection of literal and ironic statements across groups. Whereas HC showed a negativity bias when implicitly asked about the literalness of the statement, patients with BPD perceived praising utterances as less praising when explicitly asked about their perceived intention. Neither empathy nor schizotypy explained outcomes beyond borderline symptoms.

Conclusions

This was the first study to show lower detection of verbal irony in patients with BPD. While patients were less biased when asked about the literality of a statement, they perceived praising remarks as less positive on explicit measurements. The results highlight the importance of congruent, transparent communication in promoting epistemic trust in individuals with BPD.
Long-term efficacy with deep brain stimulation of the globus pallidus internus in cervical dystonia: a retrospective monocentric study
Authors: Jacksch Clemens , Zeuner Kirsten E. , Helmers Ann-Kristin , Witt Karsten , Deuschl Günther , Paschen Steffen
Published: October 2022

Background

Cervical dystonia (CD) is characterized by involuntary contractions of the cervical muscles. Data on long-term effectiveness of deep brain stimulation (DBS) are rare. The aim of this study was to evaluate the longitudinal ten years treatment efficacy of DBS in the globus pallidus internus (GPI).

Methods

A retrospective single-center data analysis was performed on patients with idiopathic CD, who were treated with GPI DBS for at least 10 years. TWSTR severity score and individual sub-items were compared between pre and post DBS surgery (n = 15) over time.

Results

There was a significant and persistent positive effect regarding the severity of TWSTRS between the conditions immediately before and 1, 5, and 10 years after establishment of GPI DBS (mean difference: 6.6–7 ± 1.6). Patients with increasing CD complexity showed a poorer response to established treatment forms, such as injection of botulinum toxin and were thus DBS candidates. Especially a predominant torticollis was significantly improved by DBS.

Conclusion

GPI DBS is an effective procedure especially in severely affected patients with a positive 10-year outcome. It should be considered in more complex CD-forms or predominant torticollis.
Hypnotherapy and therapeutic suggestion: bridging the gap between evidence and utility
Authors: Orewa Henry , Udo Itoro
Published: October 2022

The use of hypnotherapy in psychiatry has been controversial. However, evidence presented by Chan and colleagues shows that it is beneficial to the promotion of good mental health and well-being, specifically being applicable in the management of mental disorders. But what does this mean for practice? This commentary looks at what we agree and disagree with, what we opine is missing from the article and what now needs to happen. Patients should be able to access hypnotherapy or hypnosis routinely on the National Health Service. Since it works, who may it work for and how may we make this available to those who could benefit from it?
Targeting Tumor Hypoxia Inhibits Aggressive Phenotype of Dedifferentiated Thyroid Cancer
Authors: Ma Ben , Wen Shishuai , Luo Yi , Zhang Tingting , Yang Yichen , Shen Cenkai , Zhang Yan , Ji Qinghai , Qu Ning , Wang Yu
Published: October 2022

Context

Hypoxia is commonly observed in multiple aggressive cancers. Its role remains unclear in the biology and therapy of dedifferentiated thyroid cancer (DDTC).

Objective

We aimed to elucidate hypoxia's roles in DDTC tumor biology.

Methods

We discovered and confirmed hypoxia's correlation with dedifferentiation status, poor prognoses, and immune checkpoints in thyroid cancer using transcriptome data from our center and Gene Expression Omnibus (GEO) database. Then, the effect of targeting hypoxia was investigated via treating anaplastic thyroid cancer (ATC) cells with acriflavine (ACF) in vitro and in vivo, and hypoxia was analyzed for its association with response to immunotherapy in patients.

Results

Hypoxia score was positively associated with dedifferentiation status, and high hypoxia score significantly correlated with reduced overall survival, TP53 mutation, and elevated expression of immunosuppression-related markers in DDTC. ACF and siRNA targeting HIF-1α significantly suppressed growth and proliferation of thyroid cancer cells in vitro and in vivo, and reduced c-MYC and PDL1 expression in ATC. HIF-1α showed a positive correlation with PDL1 expression in DDTC. Integrated analyses of phosphoproteome and RNA sequencing data revealed that ACF's target was connected with differentiation genes and immune checkpoints via tumor-related kinases in ATC. Furthermore, hypoxia score was associated with immunotherapeutic response in some cancer types.

Conclusion

Hypoxia score serves as a significant indicator for dedifferentiation status, prognoses, and immunotherapeutic response predicted by Tumor Immune Dysfunction and Exclusion in DDTC patients. Targeting hypoxia by ACF is useful to alleviate aggressive phenotype of ATC in a preclinical model of DDTC.
Age at Menarche Mediating Visceral Adipose Tissue's Influence on Pre-eclampsia: A Mendelian Randomization Study
Authors: Deng Peizhi , Yu Qingwei , Tang Haibo , Lu Yao , He Yingdong
Published: October 2022

Context

The association between visceral adipose tissue (VAT) and pre-eclampsia (PE) shows inconsistent results and the underlying mediator remains unknown.

Objective

We aimed to explore the causal effect of VAT on PE risks and the mediation role of age at menarche (AAM) in explaining this relationship.

Methods

Summary data for PE were obtained from the FinnGen genome-wide association study (3556 cases and 114 735 controls). For exposure data, 70 genetic variants associated with the predicted VAT in 161 149 European women from UK Biobank were used as instrumental variables. Inverse variance weighted and multiple sensitivity analyses were applied. We also conducted multivariable Mendelian randomization (MR) analyses to test the association between VAT-associated single-nucleotide variations and PE. Next, mediation analyses were performed to study whether the association between VAT and PE was mediated via AAM.

Results

In univariable MR analysis, higher volume of VAT was associated with the advancement of AAM and increased PE risk (beta = −0.33; 95% CI, −0.49 to −0.16 for AAM; odds ratio 1.65, 95% CI, 1.23 to 2.20 for PE). After adjusting for waist circumference, waist to hip ratio, and hip circumference, the multivariable MR results presented the consistent positive causality of VAT on PE. Two-step MR analysis proved an estimated 14.3% of the positive effect of VAT on PE was mediated by AAM.

Conclusion

Our findings provided evidence of the causal relationship between VAT and PE and proved VAT could accelerate AAM and then contribute to the risk of incident PE.
La France et les investissements directs américains en France (1945–1973)
Authors: Barjot Dominique
Published: October 2022

Précis

Les années 1945 à 1973 ont été caractérisées, en France comme dans toute l'Europe occidentale, par une croissance économique exceptionnellement rapide, mais aussi par une intense américanisation. Celle-ci s'est traduite, notamment de 1958 à 1973, par un afflux massif de capitaux privés américains. Mesurer l'ampleur du phénomène suppose de croiser les approches macro- et micro-économiques. De la première, il ressort que les investissements directs américains bénéficièrent de facteurs favorables tant du côté de la demande que de celui de l'offre, d'où des résultats impressionnants. La seconde montre que les multinationales américaines s'intéressaient au marché français, mais que, confrontées à une forte opposition, elles ont dû adapter leurs stratégies, avec un inégal succès. Néanmoins ces investissements directs américains ont eu un effet plutôt positif sur la croissance française, qui explique en partie leur poids toujours important pour l’économie française d'aujourd'hui.

The years 1945 to 1973 were characterized, in France as in all of Western Europe, both by exceptionally rapid economic growth and by intense Americanization. This resulted, particularly from 1958 to 1973, in a massive influx of American private capital. Measuring the extent of the phenomenon demands both macro- and microeconomic approaches. Macroeconomic analysis demonstrates that US direct investment benefited from favorable conditions on both the demand and supply sides that produced impressive results. Microeconomic analysis reveals that American multinationals were interested in the French market but that, faced with strong opposition, they adapted their strategies with uneven success. Nevertheless, these American direct investments had a generally positive effect on French growth, which partly explains why they remain significant in the French economy today.
Security from the South
Authors: Al-Bulushi Samar , Ghosh Sahana , Grewal Inderpal
Published: October 2022

This introduction offers “security from the South” as a method and an analytic to trace the colonial continuities, the imperial geographies, and the forms of difference through which people become subjects of, resist, and shore up security regimes across the world. Rather than one overarching set of politics, practices, and ideas that constitute “security,” the essay insists on a pluriversal lens onto a world in which security regimes appear beguilingly universal. Using a transnational feminist approach, we contest the boundedness of the category of the “Global South,” instead emphasizing the fluidity between supposedly separate scales (e.g., North/South, intimate/global, etc.). Thinking across time and space allows for consideration of the ways in which the US empire has shaped practices elsewhere, but not in isolation, not without tension, and not without links to other empires. Security from the South thus encompasses imperial “war on terror” projects, but has a before and after to such projects, as security regimes across the Global South are enmeshed in longer histories of colonialism and racisms, religion, and gender/sexuality.
Can Black Lives Matter in a Black Country?
Authors: Thomas Deborah A.
Published: October 2022

This essay probes the project of security (defined as the protection of whiteness, class hierarchy, and heteropatriarchy) in relation to the desire for safety (glossed as “having somebody”). In probing this relation within a context in which police violence and extrajudicial killing are not typically seen as part of the global phenomenon of anti-Black racism, it seeks to contribute to a conversation in which raciality is not tethered to physicality, but instead is grounded in both historical-ideological and onto-epistemological phenomena that produce whiteness as the apex of humanity in the modern West. The essay explores the relation between security and safety through the rubric of diaspora in two senses—first as a phenomenon of Western modernity via plantation-based New World slavery, which catalyzed the development of enduring categories of (non)personhood and their elaboration into hierarchies of humanity; and second as a phenomenon of migration and the constitution of transnational sociocultural spheres. Diaspora, thus, generates forms of pan-Africanism and Black consciousness as much as it produces agendas related to transnational governance and global security infrastructures. The essay argues that to more complexly understand security from the South, these two notions of diaspora must be held in productive tension. In this way, security is revealed as a racializing project grounded in coloniality, even within majority Black spaces. The essay concludes by illuminating other terrains on which to build accountability and safety.
The biological diversity of coronaviruses: where will the new threat come from?
Authors: Khaitovich Alexandr , Sataieva Tatiana , Zukow Walery , Malygina Veronika , Shevkoplyas Lyudmila , Logadyr Tatiana , Kirsanova Marina , Andronovskaya Irina , Soroka Ekaterina
Published: October 2022

The recent outbreak of COVID-19 rose a new wave of interest to coronaviruses though the first coronaviruses were discovered in the first half of the XX century. That time coronaviruses were considered as a quite serious veterinary problem but they were not believed to become highly dangerous for humans. However, such ideas were revised in 2002 when SARS-CoV was transferred to human population in the Southeast Asia assumably from the bats, and later in 2012 when natural focus of the MERS-CoV was discovered in the Arabian countries. Due to the increased interest a large number of new Coronaviridae family members was revealed in the first decades of the XXI century. Since then taxonomic structures of coronaviruses underwent significant changes. This review is focused on the need for continued monitoring of the biological diversity of coronaviruses. The structural studies of coronaviruses regardless of the host species may allow us to identify early changes that can affect the evolutionary drift process of a particular HCoV species in

volved in viral transmission from bats or birds to humans.
Assessment of the Enhancement for the Excitation Emission in Porous Gan using Photoluminescence
Authors: Alquran M. Kh.
Published: October 2022

ABSTRACT: This work aims to assess the enhancement of optical properties for porous GaN nanostructures, which fabricated by Photoelectrochemical etching under different current densities. The changing of optical properties for different samples were investigated by Photoluminescence (PL) spectroscopy. A strong near band-gap-edge emission (NBE) was detected with peak energy 3.40 eV for as-grown and sample etched at 5mA/cm2, while its 3.41 and 3.42 eV for samples etched with 10 and 20mA/cm2 respectively. Also, another peak emission from the sapphire substrate at peak 1.7 eV was observed. The PL peak intensity of the porous samples have increased with increasing the porosity, while the FWHM of the near-band-edge peak was decreased in 5 and 10mA/cm2 samples compared to as-grown non-etched sample, indicated that the pore size decreased with etching current density and porosity. Finally, the change of refractive with porosity was investigated in the porous GaN nanostructure.
Different phases in non-Hermitian topological semiconductor stripe laser arrays
Authors: Chen Jingxuan , Fu Ting , Wang Yufei , Wang Xueyou , Dai Yingqiu , Qi Aiyi , Wang Mingjin , Zheng Wanhua
Published: October 2022

As a novel branch of topology, non-Hermitian topological systems have been extensively studied in theory and experiments recently. Topological parity-time (PT)-symmetric semiconductor stripe laser arrays based on the Su-Schreiffer-Heeger model are proposed. The degree of non-Hermicity can be tuned by altering the length of the cavities, and PT symmetry can be realized by patterned electrode. Three laser arrays working in different non-Hermitian phases are analyzed and fabricated. With the increasing degree of non-Hermicity, the peaks of output intensities move from the edge to the bulk. The proposed semiconductor stripe laser array can function as an active, flexible, and feasible platform to investigate and explore non-Hermitian topology for further developments in this field.
Variable electro-optic shearing interferometry for ultrafast single-photon-level pulse characterization
Authors: Kurzyna Stanisław , Jastrzębski Marcin , Fabre Nicolas , Wasilewski Wojciech , Lipka Michał , Parniak Michał
Published: October 2022

Despite the multitude of available methods, the characterization of ultrafast pulses remains a challenging endeavor, especially at the single-photon level. We introduce a pulse characterization scheme that maps the magnitude of its short-time Fourier transform. Contrary to many well-known solutions it does not require nonlinear effects and is therefore suitable for single-photon-level measurements. Our method is based on introducing a series of controlled time and frequency shifts, where the latter is performed via an electro-optic modulator allowing a fully-electronic experimental control. We characterized the full spectral and temporal width of a classical and single-photon-level pulse and successfully tested the applicability of the reconstruction algorithm of the spectral phase and amplitude. The method can be extended by implementing a phase-sensitive measurement and is naturally well-suited to partially-incoherent light.
Undersampling raster scans in spectromicroscopy for a reduced dose and faster measurements
Authors: Townsend Oliver , Gazzola Silvia , Dolgov Sergey , Quinn Paul
Published: October 2022

Combinations of spectroscopic analysis and microscopic techniques are used across many disciplines of scientific research, including material science, chemistry and biology. X-ray spectromicroscopy, in particular, is a powerful tool used for studying chemical state distributions at the micro and nano scales. With the beam fixed, a specimen is typically rastered through the probe with continuous motion and a range of multimodal data is collected at fixed time intervals. The application of this technique is limited in some areas due to: long scanning times to collect the data, either because of the area/volume under study or the compositional properties of the specimen; and material degradation due to the dose absorbed during the measurement. In this work, we propose a novel approach for reducing the dose and scanning times by undersampling the raster data. This is achieved by skipping rows within scans and reconstructing the x-ray spectromicroscopic measurements using low-rank matrix completion. The new method is robust and allows for 5 to 6-fold reduction in sampling. Experimental results obtained on real data are illustrated.
Estimation of the 3D spatial location of non-line-of-sight objects using passive THz plenoptic measurements
Authors: Sasaki Takahiro , Grossman Erich N. , Leger James R.
Published: October 2022

At THz frequencies, many building materials exhibit mirror-like reflectivity, greatly facilitating the 3D spatial location estimate of non-line-of-sight objects. Using a custom THz measurement setup that employs a high sensitivity room temperature THz sensor, we measure the spatial and angular components of the radiation from hidden objects scattered from rough walls. The three-dimensional location of a thermally elevated object can then be determined using this “light field” information together with a refocusing algorithm. We experimentally demonstrate accurate location estimates of human-like NLOS objects in realistic situations.
Magnetic dipole emission in resonant metal-dielectric-metal structures
Authors: Rab Md Afzalur , Munga John Ngugi , Noginova Natalia
Published: October 2022

We explore a possibility to control magnetic dipole emission with plasmonic cavities, placing Eu3+ emitters inside profile-modulated metal-dielectric-metal structures. Significant variations in the branching ratio of the magnetic and electric dipole transitions are observed as the function of the thickness of the intermediate layer. The experimental results are confirmed with numerical simulations which account for cavity and gap plasmon resonances and predict modifications in the spontaneous emission spectrum as the function of the gap size and a strong directionality of the emission for small thicknesses of the intermediate layer. The implications of having a competition between electric and magnetic dipole relaxation channels in Eu3+ are discussed.
Axial ratio bandwidth enhanced circularly polarized transmitarray antenna with a flat gain response
Authors: Li Xiaofeng , Wang Guangming , Liu Dan , Zhuang Yaqiang , Zheng Bin , Lian Shen , Zou Xiaojun , Cai Tong
Published: October 2022

In this paper, a novel broadband circularly polarized transmitarray antenna (CPTA) enabled by axial-ratio-improved receiver-transmitter metasurface loaded with parasitic patches is proposed. Split-ring-shaped parasitic patch is utilized to generate an additional resonant mode and significantly broaden the 3-dB axial ratio (AR) bandwidth of proposed receiver/transmitter patches from 6.64% to 15.61%. By cascading the receiver and transmitter with the same polarization and then rotating the cell, Pancharatnam-Berry phase can be exploited for providing a 2π phase shift. As verification, a CPTA prototype integrated with a self-made circularly polarized patch antenna is designed, fabricated, and measured. Experimental results show that the proposed CPTA obtains a 3-dB AR bandwidth of 27.1% from 12.1 to 15.9 GHz and an impedance bandwidth of 20.6% from 12.5 to 15.2 GHz. Additionally, it has a flat gain with a 3-dB gain bandwidth of 18.8% from 12.5 to 15.1 GHz, and a maximum gain of 25.6 dBi at 13.1 GHz is achieved. With the advantages of simple design, wide AR bandwidth, and flat gain performance, the proposed CPTA presents great potential applications in wireless systems.
Optical-field-induced surface nanobumps in near-infrared laser direct cleaning of nanoparticles on silicon
Authors: Zhang Shuowen , Wu Ling , Tang Jiyong , Kovalenko Volodymyr S. , Fan Lisha , Yao Jianhua
Published: October 2022

The evolution of surface damage in laser direct cleaning (LDC) of nanoparticulate contamination on silicon (Si) was theoretically and experimentally investigated. Nanobumps with a volcano-like shape were found in near-infrared laser cleaning of polystyrene latex nanoparticles on Si wafers. According to the finite-difference time-domain simulation and the high-resolution surface characterization, unusual particle-induced optical field enhancement in the vicinity of the interface between Si and nanoparticles is mainly responsible for the generation of volcano-like nanobumps. This work is of fundamental significance for the understanding of the laser–particle interaction during LDC and will promote the development of nanofabrication and nanoparticle cleaning applications in optics, microelectromechanical systems, and semiconductors.
From concept to reality: computing visual vortex beam interferometer for displacement measurement
Authors: Zhang Lei , Cao Jiaquan , Wu Shengyang , Liu Renhu , Wu Jingling , Yu Benli
Published: October 2022

In addition to the concept of picometer resolution, we discuss macro displacement measurement with a vortex beam interferometer. Three factors limiting large displacement measurement are resolved. Small topological charge numbers promise both high sensitivity and large displacement measurements. With a computing visual method, a virtual moiré pointer image immune to beam misalignment is proposed to calculate displacements. Interestingly, the absolute benchmark is found for cycle counting in the moiré pointer image of fractional topological charge. The vortex beam interferometer would not stop at the tiny displacement measurement in simulations. We report experimental measurements of nanoscale to hundred millimeter displacement in a vortex beam displacement measurement interferometer (DMI) for the first time, to the best of our knowledge.
Optical response of media and structures exhibiting spatial dispersion
Authors: Ossikovski Razvigor , Arteaga Oriol
Published: October 2022

We present a general method for redefining the permittivity and permeability tensors of a medium or structure exhibiting spatial dispersion (SD). The method effectively separates the electric and magnetic contributions that are intertwined in the traditional description of the SD-dependent permittivity tensor. The redefined material tensors are the ones to be used in the common methods for calculating the optical response of layered structures, thus enabling modeling of experiments in the presence of SD.
Magnitude-sensitive reaction times reveal non-linear time costs in multi-alternative decision-making
Authors: Marshall James A. R. , Reina Andreagiovanni , Hay Célia , Dussutour Audrey , Pirrone Angelo
Published: October 2022

Optimality analysis of value-based decisions in binary and multi-alternative choice settings predicts that reaction times should be sensitive only to differences in stimulus magnitudes, but not to overall absolute stimulus magnitude. Yet experimental work in the binary case has shown magnitude sensitive reaction times, and theory shows that this can be explained by switching from linear to multiplicative time costs, but also by nonlinear subjective utility. Thus disentangling explanations for observed magnitude sensitive reaction times is difficult. Here for the first time we extend the theoretical analysis of geometric time-discounting to ternary choices, and present novel experimental evidence for magnitude-sensitivity in such decisions, in both humans and slime moulds. We consider the optimal policies for all possible combinations of linear and geometric time costs, and linear and nonlinear utility; interestingly, geometric discounting emerges as the predominant explanation for magnitude sensitivity.
Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains
Authors: Hilau Sabrin , Katz Sophia , Wasserman Tanya , Hershberg Ruth , Savir Yonatan
Published: October 2022

Although closely related, bacterial strains from the same species show significant diversity in their growth and death dynamics. Yet, our understanding of the relationship between the kinetic parameters that dictate these dynamics is still lacking. Here, we measured the growth and death dynamics of 11 strains of Escherichia coli originating from different hosts and show that the growth patterns are clustered into three major classes with typical growth rates, maximal fold change, and death rates. To infer the underlying phenotypic parameters that govern the dynamics, we developed a phenomenological mathematical model that accounts not only for growth rate and its dependence on resource availability, but also for death rates and density-dependent growth inhibition. We show that density-dependent growth is essential for capturing the variability in growth dynamics between the strains. Indeed, the main parameter determining the dynamics is the typical density at which they slow down their growth, rather than the maximal growth rate or death rate. Moreover, we show that the phenotypic landscape resides within a two-dimensional plane spanned by resource utilization efficiency, death rate, and density-dependent growth inhibition. In this phenotypic plane, we identify three clusters that correspond to the growth pattern classes. Overall, our results reveal the tradeoffs between growth parameters that constrain bacterial adaptation.
mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations
Authors: Holmes Alexandra O. M. , Goldman Adrian , Kalli Antreas C.
Published: October 2022

Membrane-integral pyrophosphatases (mPPases) are membrane-bound enzymes responsible for hydrolysing inorganic pyrophosphate and translocating a cation across the membrane. Their function is essential for the infectivity of clinically relevant protozoan parasites and plant maturation. Recent developments have indicated that their mechanism is more complicated than previously thought and that the membrane environment may be important for their function. In this work, we use multiscale molecular dynamics simulations to demonstrate for the first time that mPPases form specific anionic lipid interactions at 4 sites at the distal and interfacial regions of the protein. These interactions are conserved in simulations of the mPPases fromThermotoga maritima,Vigna radiataandClostridium leptumand characterised by interactions with positive residues on helices 1, 2, 3 and 4 for the distal site, or 9, 10, 13 and 14 for the interfacial site. Due to the importance of these helices in protein stability and function, these lipid interactions may play a crucial role in the mPPase mechanism and enable future structural and functional studies.
The value of confidence: Confidence prediction errors drive value-based learning in the absence of external feedback
Authors: Ptasczynski Lena Esther , Steinecker Isa , Sterzer Philipp , Guggenmos Matthias
Published: October 2022

Reinforcement learning algorithms have a long-standing success story in explaining the dynamics of instrumental conditioning in humans and other species. While normative reinforcement learning models are critically dependent on external feedback, recent findings in the field of perceptual learning point to a crucial role of internally generated reinforcement signals based on subjective confidence, when external feedback is not available. Here, we investigated the existence of such confidence-based learning signals in a key domain of reinforcement-based learning: instrumental conditioning. We conducted a value-based decision making experiment which included phases with and without external feedback and in which participants reported their confidence in addition to choices. Behaviorally, we found signatures of self-reinforcement in phases without feedback, reflected in an increase of subjective confidence and choice consistency. To clarify the mechanistic role of confidence in value-based learning, we compared a family of confidence-based learning models with more standard models predicting either no change in value estimates or a devaluation over time when no external reward is provided. We found that confidence-based models indeed outperformed these reference models, whereby the learning signal of the winning model was based on the prediction error between current confidence and a stimulus-unspecific average of previous confidence levels. Interestingly, individuals with more volatile reward-based value updates in the presence of feedback also showed more volatile confidence-based value updates when feedback was not available. Together, our results provide evidence that confidence-based learning signals affect instrumentally learned subjective values in the absence of external feedback.
“How dare you?”—The normative challenge posed by Fridays for Future
Authors: Spaiser Viktoria , Nisbett Nicole , Stefan Cristina G.
Published: October 2022

Meeting the Paris Agreement will require unprecedented social change that goes hand in hand with technological and economic innovations. Research suggests that normative change, the change in what is perceived as normal or morally acceptable, can drive wider large-scale social change, i.e., change in legislation, policy, and behaviour. Normative change often starts with a normative challenge, i.e., practices considered normal, come to be seen as morally repugnant. In this paper we explore the normative challenge posed by Fridays for Future, analysing computationally a large data set of tweets in the context of this protest movement to understand the normative framework that challenges business as usual. We show that Friday for Future’s normative framework makes the shared, unjust casualty experience of young people because of the unmitigated climate crisis accessible to the public. The victims are now in spatial, temporal, and social proximity, they are our children and grandchildren, and this makes the normative challenge of the status quo (continuation of fossil-fuel based economy) so potent. The normative framework references human rights and duty of care when establishing an anti-fossil-fuel norm and prescribes solidarity with climate victims in the Global South, activism and seeking solutions that are based in science.
Adolescent support club attendance and self-efficacy associated with HIV treatment outcomes in Tanzania
Authors: Antelman Gretchen , Jahanpour Ola , Machalo Thomas , Audi Cosette , van de Ven Roland , Rutaihwa Mastidia , Lankiewicz Elise , Baird Sarah
Published: October 2022

HIV treatment outcomes may be improved by ameliorating psychosocial challenges adolescents living with HIV (ALHIV) face. This analysis describes participation in existing facility-based adolescent clubs and the associations between club attendance, adolescent well-being and HIV treatment outcomes. Data were collected through interviews with a sub-sample of adolescents age 10–19 years and medical record abstraction of all adolescents attending HIV services at seven clinics in Tanzania. Independent variables included adolescent club attendance, self-esteem, self-efficacy, mental distress, social capital and other health utilization or HIV experience characteristics. Study outcomes included visit adherence, viral suppression (<1000 cp/ml), and retention. Of 645 adolescents attending HIV services, 75% attended clubs at least once with a median of eight club sessions attended over a two-year period. Mental distress was prevalent, with 67% of the adolescents scoring above a recognized cut-off of ≥5. Adolescents who attended 10 or more clubs, compared to those not attending any clubs over a two-year period were at an almost three-fold increased odds of having good visit adherence (odds ratio [OR] 2.72, 95% confidence interval [CI]: 1.25, 5.94). Club attendance was also associated with sustained retention in the following year: adolescents who attended some clubs (1–9) had three-times the odds of being retained (OR 3.01; 95%CI: 1.86, 4.87) while those who attended 10+ had over seven-times the odds (OR 7.29; 95%CI: 4.34, 12.22). Among the 154 adolescents who were interviewed, being in the top self-efficacy tertile was positively associated with viral suppression (OR 3.04, 95%CI: 1.08, 8.60) and retention (OR 4.44, 95%CI: 1.19, 17.40). Attending the HIV clinic with a guardian/treatment supporter (OR 3.29, 95%CI: 1.17, 9.22) was also associated with viral suppression. Self-efficacy, social capital and treatment support are associated with better health outcomes among adolescents. However, many ALHIV either never attended or did not regularly attend clubs.