bluuebunny/crossref_metadata_2025 huggingface dataset:
Supervised poststack 3D seismic data classification via multiscale and multilabel consistent feature reduction
Authors: Cui Xuepeng , Huang Handong , Hao Yaju , Li Lei , Luo Yaneng , Zeng Jing , Tian Zhongbin , Shen Youyi , Hu Yangming
Published: December 2022

Following the advancement of machine learning-based seismic feature classification techniques for complex reservoirs, the acquisition and analysis of reliable seismic samples involved in seismic facies analysis and network-based inversion have emerged as a current research hotspot in the field of intelligent seismic processing. Many investigations focus on the improvement of model classification algorithms and neural networks. However, creating and collecting labels for massive seismic data are highly time-consuming and laborious, and suffer from sample unreliability and category imbalance in the case of small-sample labels. To address such problems, a multiscale and multilabel consistent principal component analysis-linear discriminant analysis (PCA-LDA) algorithm to learn a robust feature discriminative dictionary for classification is presented. In addition to the automatic use of multilabels from well logs and core analysis, we have associated multiscale with well trajectory locations to enrich sample information and enhance the reliability of the samples during 3D sample acquisition. More specifically, we begin by proposing an approach for the automatic collection of multiscale multilabel 3D poststack seismic samples along the well track. Next, the multilabel sequence in the scan window is fed into the Boyer-Moore majority vote algorithm for sample segmentation, which constructs multilabel hierarchies for each sample. Then to enhance the model training bias due to small-sample label imbalance, we develop a novel label-shuffling balanced strategy, which obtains a complete database by filling random unduplicated augmented training samples (spatial and frequency-domain augmentation operations). Finally, the linear robustness decision-making space of PCA-LDA is obtained using the feature mapping space of PCA, as well as its visual representation. Experimental results on synthetic and field seismic data demonstrate that robust feature extraction with a trustworthy and complete multiscale and multilabel sample database increases classification accuracy.
Evaluating Disease-specific Survival Prediction of Risk Stratification and TNM Systems in Differentiated Thyroid Cancer
Authors: van Velsen Evert F S , Peeters Robin P , Stegenga Merel T , van Kemenade Folkert J , van Ginhoven Tessa M , van Balkum Mathé , Verburg Frederik A , Visser W Edward
Published: December 2022

Background

Many countries have national guidelines for the management of differentiated thyroid cancer (DTC), including a risk stratification system to predict recurrence of disease. Studies whether these guidelines could also have relevance, beyond their original design, in predicting survival are lacking. Additionally, no studies evaluated these international guidelines in the same population, nor compared them with the TNM system. Therefore, we investigated the prognostic value of 6 stratification systems used by 10 international guidelines, and the TNM system with respect to predicting disease-specific survival (DSS).

Methods

We retrospectively studied adult patients with DTC from a Dutch university hospital. Patients were classified using the risk classification described in the British, Dutch, French, Italian, Polish, Spanish, European Society of Medical Oncology, European Thyroid Association, the 2009 and 2015 American Thyroid Association (ATA) guidelines, and the latest TNM system. DSS was analyzed using the Kaplan-Meier method, and the statistical model performance using the C-index, Akaike information criterion, Bayesian information criterion, and proportion of variance explained.

Results

We included 857 patients with DTC (79% papillary thyroid cancer, 21% follicular thyroid cancer). Median follow-up was 9 years, and 67 (7.8%) died because of DTC. The Dutch guideline had the worst statistical model performance, whereas the 2009 ATA/2014 British guideline had the best. However, the (adapted) TNM system outperformed all stratification systems.

Conclusions

In a European population of patients with DTC, of 10 international guidelines using 6 risk of recurrence stratification systems and 1 mortality-based stratification system, our optimized age-adjusted TNM system (8th edition) outperformed all other systems.
Central Irisin Signaling Is Required for Normal Timing of Puberty in Female Mice
Authors: Decourt Caroline , Evans Maggie C , Inglis Megan A , Anderson Greg M
Published: December 2022

Timing of puberty requires exquisite coordination of genes, hormones, and brain circuitry. An increasing level of body adiposity, signaled to the brain via the fat-derived hormone leptin, is recognized as a major factor controlling puberty onset. However, it is clear that leptin is not the only metabolic cue regulating puberty, and that developmental regulation of this process also involves tissues other than adipose, with muscle development potentially playing a role in the timing of puberty. The proteolytic processing of fibronectin type 3 domain-containing protein 5 (FNDC5) releases a hormone, irisin. Irisin is primarily produced by muscle and is released into circulation, where levels increase dramatically as puberty approaches.

We investigated the effects of a global deletion of the Fndc5 gene on pubertal timing. The absence of irisin induced a delay in puberty onset in female knockout mice compared with controls, without affecting body weight or gonadotropin-releasing hormone (GnRH) neuronal density. We next treated pre-pubertal wild-type male and female mice with an irisin receptor antagonist, cilengitide, for 7 days and observed a delay in first estrus occurrence compared to vehicle-treated control mice. Male puberty timing was unaffected. Next, we deleted the irisin receptor (integrin subunit alpha V) in all forebrain neurons and found a delay in the occurrence of first estrus in knockout females compared to controls. Taken together, these data suggest irisin plays a role in the timing of puberty onset in female mice via a centrally mediated mechanism.
Molecular Mechanisms of PTH/PTHrP Class B GPCR Signaling and Pharmacological Implications
Authors: Vilardaga Jean-Pierre , Clark Lisa J , White Alex D , Sutkeviciute Ieva , Lee Ji Young , Bahar Ivet
Published: December 2022

The classical paradigm of G protein-coupled receptor (GPCR) signaling via G proteins is grounded in a view that downstream responses are relatively transient and confined to the cell surface, but this notion has been revised in recent years following the identification of several receptors that engage in sustained signaling responses from subcellular compartments following internalization of the ligand–receptor complex. This phenomenon was initially discovered for the parathyroid hormone (PTH) type 1 receptor (PTH1R), a vital GPCR for maintaining normal calcium and phosphate levels in the body with the paradoxical ability to build or break down bone in response to PTH binding. The diverse biological processes regulated by this receptor are thought to depend on its capacity to mediate diverse modes of cyclic adenosine monophosphate (cAMP) signaling. These include transient signaling at the plasma membrane and sustained signaling from internalized PTH1R within early endosomes mediated by PTH. Here we discuss recent structural, cell signaling, and in vivo studies that unveil potential pharmacological outputs of the spatial versus temporal dimension of PTH1R signaling via cAMP. Notably, the combination of molecular dynamics simulations and elastic network model–based methods revealed how precise modulation of PTH signaling responses is achieved through structure-encoded allosteric coupling within the receptor and between the peptide hormone binding site and the G protein coupling interface. The implications of recent findings are now being explored for addressing key questions on how location bias in receptor signaling contributes to pharmacological functions, and how to drug a difficult target such as the PTH1R toward discovering nonpeptidic small molecule candidates for the treatment of metabolic bone and mineral diseases.
The adult Drosophila testis lacks a mechanism to replenish missing niche cells
Authors: Hétié Phylis , de Cuevas Margaret , Matunis Erika L.
Published: December 2022

The adult Drosophila testis contains a well-defined niche created by a cluster of hub cells, which secrete signals that maintain adjacent germline stem cells and somatic cyst stem cells (CySCs). Hub cells are normally quiescent in adult flies but can exit quiescence, delaminate from the hub and convert into CySCs after ablation of all CySCs. The opposite event, CySC conversion into hub cells, was proposed to occur under physiological conditions, but the frequency of this event is debated. Here, to probe further the question of whether or not hub cells can be regenerated, we developed methods to genetically ablate some or all hub cells. Surprisingly, when flies were allowed to recover from ablation, the missing hub cells were not replaced. Hub cells did not exit quiescence after partial ablation of hub cells, and labeled cells from outside the hub did not enter the hub during or after ablation. Despite its ability to exit quiescence in response to CySC ablation, we conclude that the hub in the adult Drosophila testis does not have a mechanism to replenish missing hub cells.
Isolation of a novel missense mutation in insulin receptor as a spontaneous revertant in ImpL2 mutants in Drosophila
Authors: Banzai Kota , Nishimura Takashi
Published: December 2022

Evolutionarily conserved insulin/insulin-like growth factor (IGF) signaling (IIS) correlates nutrient levels to metabolism and growth, thereby playing crucial roles in development and adult fitness. In the fruit fly Drosophila, ImpL2, an ortholog of IGFBP7, binds to and inhibits the function of Drosophila insulin-like peptides. In this study, we isolated a temperature-sensitive mutation in the insulin receptor (InR) gene as a spontaneous revertant in ImpL2 null mutants. The p.Y902C missense mutation is located at the functionally conserved amino acid residue of the first fibronectin type III domain of InR. The hypomorphic InR mutant animals showed a temperature-dependent reduction in IIS and body size. The mutant animals also exhibited metabolic defects, such as increased triglyceride and carbohydrate levels. Metabolomic analysis further revealed that defects in InR caused dysregulation of amino acid and ribonucleotide metabolism. We also observed that InR mutant females produced tiny irregular-shaped embryos with reduced fecundity. In summary, this novel allele of InR is a valuable tool for the Drosophila genetic model of insulin resistance and type 2 diabetes.
Evaluating the effect of digital technology on the learning of orthodontic cephalometric measurement
Authors: Yu Xin , Tian Yu , Li Dandan , Sun Wen , Wang Hua , Yuan Siyang , Yan Bin , Wang Lin , Pan Yongchu
Published: December 2022

Background: This study aimed to evaluate the effect of applying digital technology in cephalometric measurement teaching and students’ acceptance towards it.

Methods: In total, 94 undergraduates of stomatology were recruited and randomly allocated to two groups. According to the cross-over design, both groups completed cephalometric measurements through the traditional hand-drawn method and digital technology (the Dolphin software) in different orders. By traditional hand-drawn method, students need to depict the outlines of the craniofacial anatomical structures on the sulfuric transfer paper first, then marked the measurement points and completed the measurement of line spacings and angles. By digital technology, they should mark the points in the software and adjust the automatically generated outlines of the structures and obtained the results. Besides, an online questionnaire was designed to investigate students' attitudes toward the digital technology. Two professional orthodontists were invited as instructors. They measured a lateral cranial radiograph by two methods with one week’s interval, and their intra- and inter-class correlation coefficient were measured. The means of their measurements were set as standards.

Results: The inter- and intra-ICC of two instructors surpassed 90%, and there were no significant differences between their measurements, and the measurements by two methods. There were significant differences of students’ measurements (P1-SNA<0.01, P1-SNB=0.01 and P1-L1-NB (mm)<0.01; SNA: sella-nasion-subspinale angle, SNB: sella-nasion-supramental angle, L1-NB (mm): the distance from the lower central incisor tip to the nasion-supramental plane) between the traditional method and digital technology. Besides, the most results of digital technology were closer to the standards than those of traditional method, including five items with statistical significance (P2-SNB<0.05, P2-L1-NB (mm)<0.01, P2-FMA<0.05, P2-FMIA<0.05, P2-IMPA<0.01), while three items were the opposite (P2-SNA<0.05, P2-ANB (mm)<0.01, P2-NA-PA<0.01). The questionnaire showed more students preferred digital technology (33%) compared with traditional method (2%) and 72% of participants mastered 50-80% of cephalometric knowledge after the course.
Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces
Authors: Raimondi Francesco , Burkhart Joshua G. , Betts Matthew J. , Russell Robert B. , Wu Guanming
Published: December 2022

Background: Considering protein mutations in their biological context is essential for understanding their functional impact, interpretation of high-dimensional datasets and development of effective targeted therapies in personalized medicine.

Methods: We combined the curated knowledge of biochemical reactions from Reactome with the analysis of interaction-mediating 3D interfaces from Mechismo. In addition, we provided a software tool for users to explore and browse the analysis results in a multi-scale perspective starting from pathways and reactions to protein-protein interactions and protein 3D structures.

Results: We analyzed somatic mutations from TCGA, revealing several significantly impacted reactions and pathways in specific cancer types. We found examples of genes not yet listed as oncodrivers, whose rare mutations were predicted to affect cancer processes similarly to known oncodrivers. Some identified processes lack any known oncodrivers, which suggests potentially new cancer-related processes (e.g. complement cascade reactions). Furthermore, we found that mutations perturbing certain processes are significantly associated with distinct phenotypes (i.e. survival time) in specific cancer types (e.g. PIK3CA centered pathways in LGG and UCEC cancer types), suggesting the translational potential of our approach for patient stratification. Our analysis also uncovered several druggable processes (e.g. GPCR signalling pathways) containing enriched reactions, providing support for new off-label therapeutic options.

Conclusions: In summary, we have established a multi-scale approach to study genetic variants based on protein-protein interaction 3D structures. Our approach is different from previously published studies in its focus on biochemical reactions and can be applied to other data types (e.g. post-translational modifications) collected for many types of disease.
THE ROLE AND RISKS OF ESG TRANSFORMATION OF COMPANIES IN THE FACE OF NEW CHALLENGES
Authors: Vetrova Maria A.
Published: December 2022

The development of supranational and national legislation, standardization requirements and the expansion of producer responsibility have led to the formation of a new approach for the goal-setting of enterprises with a focus not only on purely commercial goals of the short-term period, but on long-term sustainability. This is how the concept of ESG principles of the enterprise was formed, which focuses the company on high efficiency of corporate governance along with the achievement of social and environmental goals of doing business. However, the institutional environment for the effective implementation of ESG practices is at the stage of formation, so there are opportunities for additional risks and threats, among which greenwashing and ESG rating errors stand out due to the lack of standardization and uniform criteria for evaluating companies, green financing errors and the emergence of a financial bubble and other risks.

The goal is to systematize the benefits of ESG transformation of companies to ensure sustainability and economic efficiency, analyze the green finance market as a key link in the transformation of sustainable initiatives into real economic benefits, analyze the risks of non-acceptance and manipulation of ESG factors for the sustainable development of companies.

Methods and tools of institutional, sectoral analysis and strategic management, theoretical approaches within the framework of the concept of sustainable development, circular and carbon neutral economy were used.

Results and scope of their application. The results of this study can be used by enterprises in the implementation of ESG principles and non-financial reporting on environmental, social and managerial risk management, by public authorities in the development of long-term sustainable development strategies and the formation of an institutional environment to achieve climate neutrality, implement energy transition, and ensure the long-term competitiveness of Russian companies in conditions of increasing global threats and the tightening of national and supranational legislation.
Czy u schyłku XVIII wieku miasta leżące w najdalej na wschód wysuniętej części Galicji rzeczywiście były miastami?
Authors: Ślusarek Krzysztof
Published: December 2022

Ostatnie ćwierćwiecze XVIII w. to w dziejach Galicji czas intensywnych reform ustrojowych. Najważniejsze z nich dotyczyły m.in. prawnego położenia ludności chłopskiej, szlachty i duchowieństwa, organizacji aparatu administracyjnego i skarbowego, a przede wszystkim systemu poboru podatków. Reformy te zapoczątkowały proces głębszych zmian, które objęły wiele dziedzin życia społecznego, politycznego i gospodarczego. Wpłynęły one także na miasta, co po kilkudziesięciu latach doprowadziło do ograniczenia liczby miejscowości oficjalnie uznawanych za miasta lub miasteczka.
Nieznany dokument Mieszka Plątonogiego z 1207–1211 r. Zbrojny powrót synów Władysława Wygnańca na Śląsk
Authors: Kowalski Marek Daniel
Published: December 2022

Artykuł zawiera edycję i analizę nieznanego źródła z czasów Mieszka Plątonogiego, z lat 1207–1211, znajdującego się w kodeksie proweniencji dominikańskiej z XV w., o sygn. Lat. I F 212, z Rosyjskiej Biblioteki Narodowej w Petersburgu. Dokument (lub zapiska) zawiera tekst potwierdzenia przez księcia Mieszka Plątonogiego, że kościół św. Wojciecha we Wrocławiu należy do klasztoru kanoników regularnych na Piasku we Wrocławiu. W książęcej konfirmacji wspomniano, że między wracającymi na Śląsk (w 1163 r.) synami Władysława Wygnańca a panującymi w Polsce ich stryjami Bolesławem Kędzierzawym i Mieszkiem Starym doszło do wojny. Bolesław Wysoki i Mieszko Plątonogi pokonali stryjów w bitwie pod Modlikowicami. Informacja ta jest sprzeczna z utrwalonym w historiografii poglądem o pokojowym powrocie Władysławowiców do ojczyzny.
“El derecho de competencia contribuye a que los países sean más prósperos”
Authors: Gutiérrez Juan David , García Bonilla Carlos
Published: December 2022

Para lograr que los mercados operen de manera efectiva y justa, el rol que juega el derecho de competencia es vital, sobre todo para economías emergentes como la nuestra. Entrevista a Juan David Gutiérrez, profesor de la Facultad de Estudios Internacionales, Políticos y Urbanos del Rosario.
Inventory Of Predatory Insects In Banana Germplasm Umbulharjo Yogyakarta
Authors: Putra Ichsan , Sahnan Hastin Nur Samsia
Published: December 2022

One  of  the  beneficial  insects  in  agriculture  and  plantations  is a predator. Using natural predators  to  control pests and diseases certainly has advantages. The purpose of this study was to calculate the level of predatory insect diversity in banana germplasm plantations and find the most abundant and least abundant predatory insects. The independent variable in this study is the banana germplasm plantation area, and the dependent variable in this study is the diversity and dominance of predatory insects found in the research location. Sampling in this study using a random method. The sweep net was in the morning, while the pitfall was collected, installed in the morning and taken in the afternoon. Predatory insect data analysis used in this study is to use the scan now-wiener diversity index and the Simpson dormancy index. The results showed that the predatory insects that mainly were found were the species, Paratrechina longicornis while the least that was found was the species Ischiodon scutellaris. From other results, namely the level of predatory insect diversity obtained, the results show that Yogyakarta banan germ plantation have moderate diversity of predatory insects. The conclusion of this study is that there is a disturbance in the Giwangan Banana Germplasm Garden Yogyakarta due to insects, so that the diversity index is moderate, while the predominance of predatory insects is 0.484, which means that in the ecosystem, one predatory insect is found that dominates.
The Effect of Arabica Coffee Fruit Skin Extract (Coffea arabica L.) on the Histopathology of Mice (Mus musculus L.) Liver Induced by Ethanol
Authors: Cahyani Dini , Maliza Rita , Setiawan Haris
Published: December 2022

Excessive alcohol consumption can lead to serious live injury. Alcohol is a source of free radicals that can cause oxidative stress. The provision of antioxidants can counter the effects of free radicals that enter the body. The skin of the Arabica coffee fruit contains antioxidant compounds that can be used as a hepatoprotective in the liver. The skin of the Arabica coffe fruit contains antioxidant compounds that may have a hepatoprotective effect on the liver. This study aimed to determine the effect of extract of arabica coffee fruit skin on necrosis, infiltration and haemorrhage in the liver tissue of 15% EtOH-induced mice for 15 days. The animals used for this study were eight weeks old male Balb/c strain mouse weighing approximately 30-40 grams. This research is an experimental study. There were five groups: the control group (K), the 15% ethanol treatment group (E), and the ethanol-induced group and given different doses of arabica coffee skin extract: 125 mg/kg BW. (A), 250 mg / kg BW (B) and 500 mg / kg BW (C). Observation and identification of necrosis, hepatocyte infiltration and haemorrhage were carried out by using Hematoxylin-eosin staining. The data analysis used was One way ANOVA and continued by Duncan Multiple Range Test (DMRT). The histopathological observations showed that the extract of arabica coffee fruit skin at a 250 mg/kg BW dose reduced the number of cell necrosis. There was no infiltration of inflammatory and hemorrhagic cells in the liver of 15% EtOH-induced mice. This study concludes that the extract of the skin of the Arabica coffee fruit has hepatoprotective potential in 15% EtOH-induced mice.
Prevalence and Intensity of Anchor Worm (Lernaea cyprinacea L.) Ectoparasite in Koi Fish (Cyprinus carpio L.) at Bantul Koi Farm D.I. Yogyakarta
Authors: Afriandini Wida , Suwartiningsih Nurul
Published: December 2022

One obstacle in the cultivation of Koi fish (Cyprinus carpio L.) in Bantul Koi Farm D.I. Yogyakarta is a disease caused by parasites of anchor worms (Lernaea cyprinacea L.). Therefore, this study observed the prevalence and intensity of anchor worm ectoparasites in Koi fish in Bantul Koi Farm. Taking fish samples using the purposive sampling technique. Each of three fish individuals was taken as replication from three populations, namely Showa, Shiro and Saragoi, with a size of 28-36 cm. The prevalence and intensity are determined by the observation method by counting the number of anchor worms found. Inferential statistics carried out data analysis of the number of ectoparasites in each population. The results showed that the highest anchor tick ectoparasite prevalence was found in the Shiro population (100%) and the lowest in the Saragoi population (33%). The highest intensity was in the Showa population (4 individu/ fish), and the lowest was in the Shiro population (2 individu/ fish), although all of them were in a low category. The highest number of ectoparasites was obtained from the Showa population (8 individuals) and the lowest in the Saragoi population (3 individuals), but it was not statistically significant. The high prevalence in the Shiro population is due to the high stocking density. Anchor flea ectoparasites attacked the skin and fins of Koi fish and were not found to attack gills. The conclusion of this study is the highest prevalence of anchor tick ectoparasites was found in the Shiro population (100%) and the lowest in the Saragoi population (33%). The highest intensity was found in the Showa population (4 individu/ fish) and the lowest in the Shiro population (2 individu/ fish), even though all of them were in a low category.
Process of Making Nata de Salacca from Honey Salak Fruit (Salacca edulis Reinw) with the Application of Biotechnology Techniques
Authors: Irwani Anisa Novia , Auranina Oskandar Yasmin , Novia Irwani Anisa , Putri Rahmawati Dian , Puri Ducha Rahmani Tara
Published: December 2022

Salak is typical Indonesian fruit commonly found in tropical countries. This fruit can fill global fruit market via exports to various countries.  One of the varieties is "salak madu" ("honey salak"), whose scientific name is (Salacca edulis Reinw), which has higher economic value than "salak pondoh super". Some of the characteristics of honey salak are thick flesh, high water content, and sweet taste. Due to its high water content, honey salak rots quickly, resulting in useless waste and causing unfavorable smell. As such, utilization of overripe salak fruit (ripe close to rotten) can be done with implementation of biotechnological approach using Acetobacter xylinum to make nata. This study is aimed at utilizing overripe honey salak (ripe close to rotten) by processing it into Nata de salaca and identifying the factors affecting the production of Nata de salaca. The study used systematic review method by reviewing and examining previously published journal articles. The results of this study suggest that overripe salak can be utilized to make Nata de Salaca with the help of Acetobacter xylinum. Based on ratio of salak substrate to water, a good Nata has the ratio of 1 : 4. 1. Whereas, based on the factor of sprout extract additive material, it is  3%. Dan Whereas based on optimum duration of fermentation, it is 10 minutes.
¿Qué género en la intervención restaurativa?
Authors: Francés Lecumberri Paz
Published: December 2022

Se parte de la confianza en la justicia restaurativa como herramienta que permita, conjuntamente con otras, despatriarcalizar la justicia y apostar por otros caminos, más afinados con las propuestas que desarrolla el feminismo abolicionista de la cuestión penal. Desde este marco, en el artículo se aborda el significado de la introducción de la perspectiva de género en las intervenciones restaurativa en el ámbito penal: mediación, conferencias y círculos, para finalmente dar algunas claves generales y específicas al respecto.
PALABRAS CLAVE. - Justicia restaurativa, feminismo abolicionista, mediación, conferencias restaurativas, círculos restaurativos.
High-order mode erbium-doped fiber laser based on cavity LPFG converters
Authors: Liu Yicong , Wang Pan , Feng Mao , Wang Qingbo , He Jiangyong , Chang Wenzhe , Wang Zhi , Liu Yange
Published: December 2022

We experimentally investigate high-order mode (HOM) generation at a
wavelength of 1.5 µm in an all-fiber erbium-doped laser based
on a long-period fiber grating (LPFG). The CW laser emission is
achieved when the pump power is above the threshold of 10 mW.
An LPFG with a 15 dB bandwidth of 147.76 nm from
1502.76 nm to 1650.52 nm is used as a mode converter
inside the cavity. The generation of the broadband

L
P

11

mode is ultimately obtained. By using
a few-mode output coupler, we can obtain the intracavity conversion of
the linear polarization mode. Single-, dual-, triple-, and
quadruple-wavelength operations can be achieved by changing the
polarization state of the polarization controllers in the cavity. The
tunable range of the output wavelengths is up to

∼

23.20

n
m

. The output power and slope
efficiency of the HOMs are presented and discussed. We believe our
work might benefit the investigation of HOM fiber lasers, and might be
further applied to the intracavity conversion of the linear
polarization mode or orbital angular momentum beams.
Using an acousto-optic modulator as a fast spatial light modulator
Authors: Liu Xialin , Braverman Boris , Boyd Robert W.
Published: December 2022

High-speed spatial light modulators (SLM) are crucial components for free-space communication and structured illumination imaging. Current approaches for dynamical spatial mode generation, such as liquid crystal SLMs or digital micromirror devices, are limited to a maximum pattern refresh rate of 10 kHz and have a low damage threshold. We demonstrate that arbitrary spatial profiles in a laser pulse can be generated by mapping the temporal radio-frequency (RF) waveform sent to an acousto-optic modulator (AOM) onto the optical field. We find that the fidelity of the SLM performance can be improved through numerical optimization of the RF waveform to overcome the nonlinear effect of AOM. An AOM can thus be used as a 1-dimensional SLM, a technique we call acousto-optic spatial light modulator (AO-SLM), which has 50 µm pixel pitch, over 1 MHz update rate, and high damage threshold. We simulate the application of AO-SLM to single-pixel imaging, which can reconstruct a 32×32 pixel complex object at a rate of 11.6 kHz with 98% fidelity.
Wavelength calibration of birefringent interferometers for 2-D measurement of plasma flow
Authors: Allcock Joseph S. , Silburn Scott A. , Sharples Ray M. , Harrison James R. , Conway Neil J. , Long Ting , Lin Nie
Published: December 2022

Imaging birefringent interferometers are used to measure plasma flow in 2-D via the Doppler shift of a spectral emission line. Applications include plasma physics study in fusion energy experiments and in the Earth’s upper atmosphere. We present a new, to the best of our knowledge, method for wavelength calibration that does not require measurement at the rest wavelength of the targeted spectral line, nor measurement using a tuneable laser source. This is useful when such light sources are not available. Fringes measured at known wavelengths from the emission lines of gas-discharge lamps are used to constrain an instrument model which can generate the required calibration data. In the process, optical path difference, dispersion and misalignments are characterized. The “2π ambiguity” of interferogram phase data is handled using circular statistics, allowing the wavelength span of the calibration lines to far exceed the unambiguous measurement range of the instrument. The technique is demonstrated to an accuracy of ±1 pm (±0.7 km/s flow-equivalent) over a 40 nm visible wavelength range.
Efficient room-temperature molecular single-photon sources for quantum key distribution
Authors: Murtaza Ghulam , Colautti Maja , Hilke Michael , Lombardi Pietro , Cataliotti Francesco Saverio , Zavatta Alessandro , Bacco Davide , Toninelli Costanza
Published: December 2022

Quantum key distribution (QKD) allows the distribution of cryptographic keys between multiple users in an information-theoretic secure way, exploiting quantum physics. While current QKD systems are mainly based on attenuated laser pulses, deterministic single-photon sources could give concrete advantages in terms of secret key rate (SKR) and security owing to the negligible probability of multi-photon events. Here, we introduce and demonstrate a proof-of-concept QKD system exploiting a molecule-based single-photon source operating at room temperature and emitting at 785 nm. With an estimated maximum SKR of 0.5 Mbps, our solution paves the way for room-temperature single-photon sources for quantum communication protocols.
Actively tunable linear and circular dichroic metamirrors based on single-layer graphene
Authors: Xu Jie , Tang Jian , Chen Ming , Teng Chuanxin , Deng Shijie , Cheng Yu , Qu Shiliang , Yuan Libo
Published: December 2022

Aiming at the problems of low efficiency, single function and complex structure of the existing dichroic metamirrors, the actively tunable linear and circular dichroic metamirrors based on single-layer graphene are proposed in this study. The designed metamirrors are mainly composed of the ion-gel, patterned graphene, polyimide, polysilicon and gold substrates. The anisotropy of the achiral structures can be used to realize circular dichroism (0.8) and linear dichroism (0.9) in two directions at the same time without functional switching. Additionally, the incidence angle of electromagnetic waves, rather than the structural chirality, is used to create the exceptionally strong dichroism. The proposed metamirrors not only increase the integration, but also reduce the angular dispersion and complexity of the structure. What's more, by changing the Fermi level of graphene, the CD function of the metamirrors can be tuned in the range of 0 - 0.8, and the LD function can be tuned in the range of 0.22 - 0.9. The designed metamirrors can achieve dual functions under a wide range of incident angles, and can be widely used in various fields such as terahertz imaging, biological detection, optical sensing, and spectrometry.
Behavior and measurement method of inter-core crosstalk in multicore fibers with core-dependent loss
Authors: Kobayashi Yuto , Hayashi Tetsuya
Published: December 2022

We quantitatively discussed the effect of core-dependent loss (CDL) on the crosstalk (XT) of multicore fibers (MCFs). In practical ranges of XT and CDL, CDL has no significant effect on power coupling coefficients and XT between cores. Therefore, taking into account the CDL-induced signal attenuation difference among cores is sufficient when considering the signal-to-XT ratio in an MCF with CDL. We also analytically investigated the effect of CDL on XT measurements, and found that the effects of the CDLs induced in an MCF as a measurement target and a measurement setup (including input/output devices) can be canceled in the geometric mean of linear values (or the arithmetic mean of decibel values) of the XT by switching the source core and destination core of the XT.
Open boundary conditions for the simulation of leaky modes
Authors: Heinz Jonathan , Kolesik Miroslav
Published: December 2022

We propose an open-boundary method for the simulation of the modes of confining dielectric structures. The technique is inclusive of normal modes, but is especially advantageous for the simulation of quasi-normal, or leaky, modes. The central idea is to utilize the asymptotic form of targeted solutions to eliminate the outer part of the computational domain and bring the numerical boundary close to the simulated structure. While a similar approach was previously demonstrated for scalar quantum models, here we put forward a generalization for fully vectorial fields. Accuracy in this new context is validated using step-index and tube-type hollow core fiber geometries. The method has broad applicability, as quasi-bound modes are intrinsic to many systems of interest in optics and photonics.
Close-kin mark-recapture methods to estimate demographic parameters of mosquitoes
Authors: Sharma Yogita , Bennett Jared B. , Rašić Gordana , Marshall John M.
Published: December 2022

Close-kin mark-recapture (CKMR) methods have recently been used to infer demographic parameters such as census population size and survival for fish of interest to fisheries and conservation. These methods have advantages over traditional mark-recapture methods as the mark is genetic, removing the need for physical marking and recapturing that may interfere with parameter estimation. For mosquitoes, the spatial distribution of close-kin pairs has been used to estimate mean dispersal distance, of relevance to vector-borne disease transmission and novel biocontrol strategies. Here, we extend CKMR methods to the life history of mosquitoes and comparable insects. We derive kinship probabilities for mother-offspring, father-offspring, full-sibling and half-sibling pairs, where an individual in each pair may be a larva, pupa or adult. A pseudo-likelihood approach is used to combine the marginal probabilities of all kinship pairs. To test the effectiveness of this approach at estimating mosquito demographic parameters, we develop an individual-based model of mosquito life history incorporating egg, larva, pupa and adult life stages. The simulation labels each individual with a unique identification number, enabling close-kin relationships to be inferred for sampled individuals. Using the dengue vector Aedes aegypti as a case study, we find the CKMR approach provides unbiased estimates of adult census population size, adult and larval mortality rates, and larval life stage duration for logistically feasible sampling schemes. Considering a simulated population of 3,000 adult mosquitoes, estimation of adult parameters is accurate when ca. 40 adult females are sampled biweekly over a three month period. Estimation of larval parameters is accurate when adult sampling is supplemented with ca. 120 larvae sampled biweekly over the same period. The methods are also effective at detecting intervention-induced increases in adult mortality and decreases in population size. As the cost of genome sequencing declines, CKMR holds great promise for characterizing the demography of mosquitoes and comparable insects of epidemiological and agricultural significance.
Is artificial intelligence capable of generating hospital discharge summaries from inpatient records?
Authors: Ando Kenichiro , Okumura Takashi , Komachi Mamoru , Horiguchi Hiromasa , Matsumoto Yuji
Published: December 2022

Medical professionals have been burdened by clerical work, and artificial intelligence may efficiently support physicians by generating clinical summaries. However, whether hospital discharge summaries can be generated automatically from inpatient records stored in electronic health records remains unclear. Therefore, this study investigated the sources of information in discharge summaries. First, the discharge summaries were automatically split into fine-grained segments, such as those representing medical expressions, using a machine learning model from a previous study. Second, these segments in the discharge summaries that did not originate from inpatient records were filtered out. This was performed by calculating the n-gram overlap between inpatient records and discharge summaries. The final source origin decision was made manually. Finally, to reveal the specific sources (e.g., referral documents, prescriptions, and physician’s memory) from which the segments originated, they were manually classified by consulting medical professionals. For further and deeper analysis, this study designed and annotated clinical role labels that represent the subjectivity of the expressions and builds a machine learning model to assign them automatically. The analysis results revealed the following: First, 39% of the information in the discharge summary originated from external sources other than inpatient records. Second, patient’s past clinical records constituted 43%, and patient referral documents constituted 18% of the expressions derived from external sources. Third, 11% of the missing information was not derived from any documents. These are possibly derived from physicians’ memories or reasoning. According to these results, end-to-end summarization using machine learning is considered infeasible. Machine summarization with an assisted post-editing process is the best fit for this problem domain.
Transcription factor binding process is the primary driver of noise in gene expression
Authors: Parab Lavisha , Pal Sampriti , Dhar Riddhiman
Published: December 2022

Noise in expression of individual genes gives rise to variations in activity of cellular pathways and generates heterogeneity in cellular phenotypes. Phenotypic heterogeneity has important implications for antibiotic persistence, mutation penetrance, cancer growth and therapy resistance. Specific molecular features such as the presence of the TATA box sequence and the promoter nucleosome occupancy have been associated with noise. However, the relative importance of these features in noise regulation is unclear and how well these features can predict noise has not yet been assessed. Here through an integrated statistical model of gene expression noise in yeast we found that the number of regulating transcription factors (TFs) of a gene was a key predictor of noise, whereas presence of the TATA box and the promoter nucleosome occupancy had poor predictive power. With an increase in the number of regulatory TFs, there was a rise in the number of cooperatively binding TFs. In addition, an increased number of regulatory TFs meant more overlaps in TF binding sites, resulting in competition between TFs for binding to the same region of the promoter. Through modeling of TF binding to promoter and application of stochastic simulations, we demonstrated that competition and cooperation among TFs could increase noise. Thus, our work uncovers a process of noise regulation that arises out of the dynamics of gene regulation and is not dependent on any specific transcription factor or specific promoter sequence.
Rapid molecular diversification and homogenization of clustered major ampullate silk genes in Argiope garden spiders
Authors: Baker Richard H. , Corvelo André , Hayashi Cheryl Y.
Published: December 2022

The evolutionary diversification of orb-web weaving spiders is closely tied to the mechanical performance of dragline silk. This proteinaceous fiber provides the primary structural framework of orb web architecture, and its extraordinary toughness allows these structures to absorb the high energy of aerial prey impact. The dominant model of dragline silk molecular structure involves the combined function of two highly repetitive, spider-specific, silk genes (spidroins)—MaSp1 and MaSp2. Recent genomic studies, however, have suggested this framework is overly simplistic, and our understanding of how MaSp genes evolve is limited. Here we present a comprehensive analysis of MaSp structural and evolutionary diversity across species ofArgiope(garden spiders). This genomic analysis reveals the largest catalog of MaSp genes found in any spider, driven largely by an expansion of MaSp2 genes. The rapid diversification ofArgiopeMaSp genes, located primarily in a single genomic cluster, is associated with profound changes in silk gene structure. MaSp2 genes, in particular, have evolved complex hierarchically organized repeat units (ensemble repeats) delineated by novel introns that exhibit remarkable evolutionary dynamics. These repetitive introns have arisen independently within the genus, are highly homogenized within a gene, but diverge rapidly between genes. In some cases, these iterated introns are organized in an alternating structure in which every other intron is nearly identical in sequence. We hypothesize that this intron structure has evolved to facilitate homogenization of the coding sequence. We also find evidence of intergenic gene conversion and identify a more diverse array of stereotypical amino acid repeats than previously recognized. Overall, the extreme diversification found among MaSp genes requires changes in the structure-function model of dragline silk performance that focuses on the differential use and interaction among various MaSp paralogs as well as the impact of ensemble repeat structure and different amino acid motifs on mechanical behavior.
Salivary gland ultrasound is associated with the presence of autoantibodies in patients with Sjögren’s syndrome: A Danish single-centre study
Authors: Schmidt Nanna Surlemont , Voss Anne , Nilsson Anna Christine , Terslev Lene , Just Søren Andreas , Lindegaard Hanne M.
Published: December 2022

Objectives

To investigate whether ultrasound findings of major salivary glands are correlated with serological markers, autoantibodies, patient- or doctor-reported disease activity in a Danish cohort of patients with primary Sjögren’s Syndrome (pSS).

Methods

In all, 49 patients at Odense University Hospital with pSS diagnosed according to the 2002 American-European Consensus Group (AECG) classification criteria were included. Patients were characterized using the EULAR Sjögren’s Syndrome Disease Activity Index (ESSDAI, score of systemic complications) and EULAR Sjögren’s Syndrome Patient Reported Index (ESSPRI), serologic markers, Schirmer’s test and salivary test. Salivary gland ultrasound (SGUS) was performed of the submandibular and parotid glands and scored according to the Outcome Measures in Rheumatoid Arthritis Clinical Trials (OMERACT) semi-quantitative scoring system.

Results

More patients with abnormal SGUS had antinuclear antibodies (ANA) (p = 0.002), anti-Ro52 (p = 0.001), anti-Ro60 (p<0.001), anti-La (p<0.001) and IgM-RF (p<0.001). Titers for ANA (p = 0.02) and anti-Ro52 (p = 0.03) were higher in patients with abnormal SGUS. Twenty-three of the pSS patients had no pathological findings on SGUS. There was no correlation between SGUS severity and ESSDAI- or ESSPRI-scores.

Conclusions

Abnormal SGUS findings are associated with autoantibodies of high specificity for pSS but not with ESSDAI, ESSPRI or inflammatory markers.
The intergenerational transmission of educational attainment: A closer look at the (interrelated) roles of paternal involvement and genetic inheritance
Authors: Verweij Renske Marianne , Keizer Renske
Published: December 2022

Numerous studies have documented a strong intergenerational transmission of educational attainment. In explaining this transmission, separate fields of research have studied separate mechanisms. To obtain a more complete understanding, the current study integrates insights from the fields of behavioural sciences and genetics and examines the extent to which paternal involvement and children’s polygenic score (PGS) are unique underlying mechanisms, correlate with each other, and/or act as important confounders in the intergenerational transmission of fathers’ educational attainment. To answer our research questions, we use rich data from The National Longitudinal Study of Adolescent to Adult Health (n = 4,579). Firstly, results from our mediation analyses showed a significant association between fathers’ educational attainment and children’s educational attainment (0.303). This association is for about 4 per cent accounted for by paternal involvement, whereas a much larger share, 21 per cent, is accounted for by children’s education PGS. Secondly, our results showed that these genetic and behavioural factors are significantly correlated with each other (correlations between 0.06 and 0.09). Thirdly, we found support for genetic confounding, as adding children’s education PGS to the model reduced the association between paternal involvement and children’s educational attainment by 11 per cent. Fourthly, evidence for social confounding was almost negligible (the association between child’s education PGS and educational attainment was only reduced by half of a per cent). Our findings highlight the importance of integrating insights and data from multiple disciplines in understanding the mechanisms underlying the intergenerational transmission of inequality, as our study reveals that behavioural and genetic influences overlap, correlate, and confound each other as mechanisms underlying this transmission.