bluuebunny/crossref_metadata_2025 huggingface dataset:
Population structure analysis of Phlebotomus papatasi populations using transcriptome microsatellites: possible implications for leishmaniasis control and vaccine development
Authors: Hamarsheh Omar , Guernaoui Souad , Karakus Mehmet , Yaghoobi-Ershadi Mohammad Reza , Kruger Andreas , Amro Ahmad , Kenawy Mohamed Amin , Dokhan Mostafa Ramadhan , Shoue Douglas A. , McDowell Mary Ann
Published: October 2024

Background

Phlebotomus papatasi is considered the primary vector of Leishmania major parasites that cause zoonotic cutaneous leishmaniasis (ZCL) in the Middle East and North Africa. Phlebotomus papatasi populations have been studied extensively, revealing the existence of different genetic populations and subpopulations over its large distribution range. Genetic diversity and population structure analysis using transcriptome microsatellite markers is important to uncover the vector distribution dynamics, essential for controlling ZCL in endemic areas.

Methods

In this study, we investigated the level of genetic variation using expressed sequence tag-derived simple sequence repeats (EST-SSRs) among field and colony P. papatasi samples collected from 25 different locations in 11 countries. A total of 302 P. papatasi sand fly individuals were analyzed, including at least 10 flies from each region.

Results

The analysis revealed a high-level population structure expressed by five distinct populations A through E, with moderate genetic differentiation among all populations. These genetic differences in expressed genes may enable P. papatasi to adapt to different environmental conditions along its distribution range and likely affect dispersal.

Conclusions

Elucidating the population structuring of P. papatasi is essential to L. major containment efforts in endemic countries. Moreover, the level of genetic variation among these populations may improve our understanding of Leishmania–sand fly interactions and contribute to the efforts of vaccine development based on P. papatasi salivary proteins.

Graphical Abstract
A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome
Authors: Kawano-Sugaya Tetsuro , Arikawa Koji , Saeki Tatsuya , Endoh Taruho , Kamata Kazuma , Matsuhashi Ayumi , Hosokawa Masahito
Published: October 2024

Background

The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.

Results

We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.

Conclusions

The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community.
Inflammatory and genomic interactions within keratoconus susceptible patients: a nationwide registered case–control study
Authors: Doroodgar Farideh , Alizadeh Fatemeh , Niazi Sana , Razavi Seyedeh Maryam , Jalilian Nazanin , Azarnezhad Asaad , Niazi Feizollah , Javadi Mohammad Ali , Alió del Barrio Jorge , Dehghani Shima , Moshirfar Majid , Gatzioufas Zisis , Ambrósio Renato , Alio Jorge L.
Published: October 2024

Purpose

This study aimed to investigate the association between variants in the interleukin (IL)-1 gene cluster and susceptibility to keratoconus (KC) in an Iranian population.

Methods

In the case group, there were 188 KC patients diagnosed by clinical findings and corneal tomography. The control group included all 205 healthy controls with no personal or family history of eye-related, metabolic, or immune system-related disease. Using the standard salting out extraction procedure, genomic DNA was isolated from peripheral blood leukocytes. The genotypes were determined by applying agarose gel electrophoresis for the IL-1RN 86 bp VNTR and polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) for rs16944 and rs1143634.

Results

The results showed a significant association between the IL-1β rs1143634 (rs1143634 T allele, P = 0.008) and IL-1RN 86 bp VNTR polymorphisms (LL and LS genotype, P = 0.048 and 0.012 respectively) and susceptibility to KC in the Iranian population. The genotype distributions of rs1143634 (P = 0.004) and rs2234663 (P = 0.042) significantly differed between case and control groups, with certain genotypes demonstrating a protective effect against KC. Logistic regression analysis revealed a protective effect of the IL-1RN L allele [odds ratio (OR) = 0.367, 95% confidence interval (CI): 0.240–0.562; P = 0.000] and certain haplotypes (OR = 0.628, 95% CI: 0.447–0.884; P = 0.007) against KC. However, no significant association was found for the IL-1β rs16944 polymorphism.

Conclusion

This study provides evidence for an association between variants in the IL-1 gene cluster and susceptibility to KC in an Iranian population. Further research on larger and more diverse populations is warranted to validate these findings and explore the underlying mechanisms involved.
Technical sandbox for a Global Patient co-Owned Cloud (GPOC)
Authors: Davids Joe , ElSharkawy Mohamed , Ashrafian Hutan , Herlenius Eric , Lidströmer Niklas
Published: October 2024

Background

The use of Cloud-based storage personal health records has increased globally. The GPOC series introduces the concept of a Global Patient co-Owned Cloud (GPOC) of personal health records. Technical sandboxes allow the capability to simulate different scientific concepts before making them production ready. None exist for the medical fields and cloud-based research.

Methods

We constructed and tested the sandbox using open-source infrastructures (Ubuntu, Alpine Linux, and Colaboratory) and demonstrated it on a cloud platform. Data preprocessing utilised standard and in-house libraries. The Mina protocol, implementing zero-knowledge proofs, ensured secure blockchain operations, while the Ethereum smart contract protocol within Hyperledger Besu supported enterprise-grade sandbox development.

Results

Here, we present the GPOC series’ technical sandbox. This is to facilitate future online research and testing of the concept and its security, encryption, movability, research potential, risks and structure. It has several protocols for homomorphic encryption, decentralisation, transfers, and file management.

The sandbox is openly available online and tests authorisation, transmission, access control, and integrity live. It invites all committed parties to test and improve the platform. Individual patients, clinics, organisations and regulators are invited to test and develop the concept.

The sandbox displays co-ownership of personal health records. Here it is trisected between patients, clinics and clinicians. Patients can actively participate in research and control their health data. The challenges include ensuring that a unified underlying protocol is maintained for cross-border delivery of care based on data management regulations.

Conclusions

The GPOC concept, as demonstrated by the GPOC Sandbox, represents an advancement in healthcare technology. By promoting patient co-ownership and utilising advanced technologies like blockchain and homomorphic encryption, the GPOC initiative enhances individual control over health data and facilitates collaborative medical research globally. The justification for this research lies in its potential to improve evidence-based medicine and AI dissemination. The significance of the GPOC initiative extends to various aspects of healthcare, patient co-ownership of health data, promoting access to resources and healthcare democratisation. The implications include better global health outcomes through continued development and collaboration, ensuring the successful adoption of the GPOC Sandbox and advancing innovation in digital health.
Medico-legal psychiatric assessments in the age of video-linking
Authors: Briscoe James
Published: October 2024

Following the COVID-19 pandemic, assessments by video link became a standard and acceptable form of medico-legal evaluation. The various challenges to achieving an accurate and robust medico-legal assessment via a remote platform are explored in this clinical reflection. It is concluded that any limitations to a remotely undertaken assessment must be highlighted to the court and an in-person assessment considered as a reasonable alternative in some cases.
La passione copta di San Filoteo di Antiochia secondo il codice M 583 di Pierpont Morgan Library a New York
Authors: Κουρεμένος Νικόλαος
Published: October 2024

Με βάση το χειρόγραφο Μ 583 που θησαυρίζεται στη Βιβλιοθήκη Pierpont Morgan της Νέας Υόρκης και λαμβάνοντας υπόψη εννέα επιπλέον κειμενικές μαρτυρίες, η παρούσα διατριβή παρουσιάζει για πρώτη φορά μια κριτική έκδοση της Κοπτικής (Σαχιδικής) εκδοχής του Μαρτυρίου του Αγίου Φιλοθέου από την Αντιοχεία, ο οποίος λέγεται ότι μαρτύρησε επί Διοκλητιανού και αποτελεί έναν από τους βασικούς χαρακτήρες της αφήγησης. Το Κοπτικό κείμενο συνοδεύεται από Ιταλική μετάφραση και κριτικές σημειώσεις.
Effect of lycopene on prostate cancer among native African men: A protocol for an open-label randomized clinical trial in Tanzania
Authors: Matumaini Hope K. , Mboya Innocent B. , Sariko Margaretha , Seif Mshangama J. , Mremi Alex , Lukambagire Abdul-Hamid , Msuya Sia E. , Mmbaga Blandina Theophil , Pisters Louis , Mteta Alfred K.
Published: October 2024

Background Prostate cancer (PCa) is the most common cancer and the fifth leading cause of death in men worldwide. The treatment of PCa depends on the clinical stage of the disease, prostate-specific antigen (PSA) level, and histology. Lycopene is a bright red carotenoid found in tomatoes, which enhances apoptosis in prostate cells, but its effectiveness has not been studied in East African countries. This study aimed to determine the effectiveness of lycopene from tomato extracts in reducing PSA levels, disease progression, and apoptosis in the prostate glands of men with PCa in Tanzania. Methods This study will be a randomized phase III clinical trial of men diagnosed with PCa in Tanzania. In total, 400 men will be randomized in a 1:1 ratio to receive intervention (n=200) and control (n=200) and followed for 12 months. The intervention arm will receive tomato paste for daily use in addition to the standard treatment, whereas the control arm will only follow the standard of care. The primary endpoints will be a reduction in PSA levels, improved clinical status, and apoptosis of the prostate gland. Data analysis was performed based on the intention-to-treat principle. Descriptive statistics were used to compare average lycopene and PSA levels in the intervention group using T-test and Chi-squared tests. Generalized linear mixed models will be used to further assess the effect of lycopene on PCa progression, urinary symptoms, and PSA reduction. All statistical tests were two-sided at an alpha level of <0.05. Discussion The study used a food supplement as a drug/intervention with minimal or no adverse reactions. However, there is a fear that the control group may not adhere to the protocol after learning the benefits of tomato paste. The study findings will promote the consumption of tomato paste in males diagnosed with PCa to improve the clinical status and reduce disease progression. Trial registration The study has been registered at the Pan African Clinical Trial Registry with registration No PACTR202405488763956.
Phytotherapy as an alternative approach in oral candidiasis management: A systematic review protocol
Authors: Bouslama Ghada , Zidani Hajer , Ben Messaoud Nour Sayda , Oualha Lamia , Ben youssef Souha
Published: October 2024

Background Conventional antifungal therapies, including topical applications, are effective against oral candidiasis but have limitations such as resistance development and cytotoxicity especially for immunocompromised patients. Phytotherapy presents a promising alternative, offering potential solutions to these challenges. However, despite numerous clinical trials, there is a lack of standardized protocols for phytotherapeutic applications. This systematic review protocol seeks to evaluate the potential of phytotherapy as an alternative treatment for oral candidiasis and compare its efficacy with standard antifungal therapies. Protocol This protocol aims to assess the effectiveness of phytotherapy compared to standard antifungal treatments for oral candidiasis. Initially, controlled descriptors in MeSH terms (e.g., “Candidiasis, Oral,” “Phytotherapy”) and keywords were selected from MEDLINE and combined using Boolean operators (‘AND’, ‘OR’) to create a comprehensive search strategy. Titles and abstracts will be screened by two independent reviewers to select studies that meet the inclusion criteria. The quality and risk of bias of the selected studies will be assessed afterward. Data will be gathered using standardized tools and subsequently synthesized for analysis. Discrepancies between reviewers will be settled through discussion, or, if required, by involving a third reviewer. Discussion Results obtained from this systematic review will describe various natural compounds like essential oils, herbal extracts, and bioactive plant ingredients that exhibit antifungal properties used against oral candidiasis and will evaluate their effectiveness in comparison to standard antifungal treatments. Systematic review registration PROSPERO: CRD42024584029 (Registered on 07/09/2024)
Algorithm for Key Transparency with Transparent Logs
Authors: Mollakuqe Elissa , Rexhepi Shasivar , Bunjaku Ridvan , Dag Hasan , Chukwu Ikechukwu John
Published: October 2024

Background Cryptography plays a crucial role in securing digital communications and data storage. This study evaluates the Transparent Key Management Algorithm utilizing Merkle trees, focusing on its performance and security effectiveness in cryptographic key handling. Methods The research employs simulated experiments to systematically measure and analyze key operational metrics such as insertion and verification times. Synthetic datasets are used to mimic diverse operational conditions, ensuring rigorous evaluation under varying workloads and security threats. Implementation is carried out using R programming, integrating cryptographic functions and Merkle tree structures for integrity verification. Results Performance analysis reveals efficient insertion and verification times under normal conditions, essential for operational workflows. Security evaluations demonstrate the algorithm's robustness against tampering, with approximately 95% of keys verified successfully and effective detection of unauthorized modifications. Simulated attack scenarios underscore its resilience in mitigating security threats. Conclusions The Transparent Key Management Algorithm, enhanced by Merkle trees and cryptographic hashing techniques, proves effective in ensuring data integrity, security, and operational efficiency. Recommendations include continuous monitoring and adaptive algorithms to bolster resilience against evolving cybersecurity challenges, promoting trust and reliability in cryptographic operations.
A protocol for a living mapping review of global research funding for infectious diseases with a pandemic potential – Pandemic PACT
Authors: Seminog Olena , Furst Rodrigo , Mendy Thomas , Rohanian Omid , Levanita Shanthi , Kadri-Alabi Zaharat , Jabin Nusrat , Humphreys Georgina , Antonio Emilia , Bucher Adrian , Norton Alice
Published: October 2024

The COVID CIRCLE initiative Research Project Tracker by UKCDR and GloPID-R and associated living mapping review (LMR) showed the importance of sharing and analysing data on research at the point of funding to improve coordination during a pandemic. This approach can also help with research preparedness for outbreaks and hence our new programme the Pandemic Preparedness: Analytical Capacity and Funding Tracking Programme (Pandemic PACT) has been established. The LMR described in this protocol builds on the previous UKCDR and GloPID-R COVID-19 Research Project database with addition of the priority diseases from the WHO Blueprint list plus initial additions of pandemic influenza, mpox and plague. We capture data on new funding commitments directly from funders and map these against a core ontology (aligned to existing research roadmaps). We will analyse regularly collated new research funding commitments to provide an open, accessible, near-real-time overview of the funding landscape for a wide range of infectious disease and pandemic preparedness research and assess gaps. The periodicity of updates will be increased in the event of a major outbreak. We anticipate that this LMR and the associated online tool will be a useful resource for funders, policy makers and researchers. In the future, our work will inform a more coordinated approach to research funding by providing evidence and data, including identification of gaps in funding allocation with a particular focus on low- and middle-income countries.
Comprehensive Literature Review of the use of The Bakri Balloon for Managing Postpartum Hemorrhage
Authors: Kowal Joanna , Połujański Paweł , Cyran Piotr , Jaroszyńska Anna , Jaroszyński Filip , Paleczny Jan , Parobczak Robert , Winciorek Joanna , Wiśniewska Adrianna
Published: October 2024

Postpartum hemorrhage (PPH) remains a significant cause of maternal mortality and morbidity worldwide. It is defined as excessive bleeding, typically more than 500 ml of blood loss within the first 24 hours after childbirth. The Bakri Balloon technique has emerged as a promising solution for managing PPH, offering a minimally invasive approach to achieving hemostasis and preventing the need for more invasive surgical procedures.
Aims: The aim of this paper review is to provide an overview of the effectiveness of intrauterine balloon tamponade in managing PPH.
Methods: We conducted this paper review by selecting articles, retrospective cohort studies and reviews from clinical trials from PubMed.
Results: Numerous studies have shown high success rates of  treating PPH using The Bakri Balloon intrauterine tamponade.
Conclusions:  The Bakri Balloon intrauterine tamponade is an effective method in the management of primary postpartum hemorrhage.
„Po raz pierwszy zobaczyła kogoś równie czarnego jak ona” – inkluzywność w przekładzie intralingwalnym baśni (na przykładzie wybranych opowiadań ze zbioru Piękno i bestie. Niebezpieczne baśnie Somana Chainaniego)
Authors: Matuszko Kinga
Published: October 2024

“IT IS THE FIRST TIME SHE’S SEEN ANYONE AS BLACK AS HER” – INCLUSIVENESS IN THE INTRALINGUAL TRANSLATION OF FAIRY TALES (BASED ON THE EXAMPLE OF SELECTED STORIES FROM THE COLLECTION BEASTS AND BEAUTY: DANGEROUS TALES BY SOMAN CHAINANI)The article analyses the refractions introduced in the retellings (intralingual translation) of fairy tales from Beasts and Beauty: Dangerous Tales by Soman Chainani. These transformations have their source in cultural translation and concern broadly understood inclusivity (e.g. change of skin colour, biological sex and sexual orientation, deconstruction of hegemonic masculinity). Possible sources of the introduced modifications were also indicated (an attempt to expand the recipient circle, representation of previously excluded minorities, but also the desire to stir emotions).
Derechos para la transformación y la dignidad en personas trans privadas de la libertad
Authors: Villamarín Mor Valentina , Bermúdez Carrillo Jorge Leonardo , Paredes Álvarez Giovanny
Published: October 2024

Las personas trans en establecimientos penitenciarios han sido sujetos sistemáticamente vulnerados por marcos sociales hegemónicos y heteronormados que establecen dinámicas binarias de relacionamiento en donde se discriminan, estigmatizan e invisibilizan las identidades de género y orientaciones sexuales diversas, siendo sus cuerpos los principales territorios receptores de violencias. Para la escritura de este libro se examinaron las experiencias de mujeres y hombres trans privados de la libertad de siete cárceles de Colombia, se analizaron las necesidades específicas, conflictos y vulneraciones, así como el conocimiento de sus derechos en marcos normativos desde una perspectiva buttom up y se crearon estrategias colectivas para la construcción de herramientas prácticas de participación desde la sensibilización y el reconocimiento con el objetivo de dignificar su experiencia en prisión.
Uso da Comunicação Não Violenta na Análise de Cenários de Conflitos em Engenharia de Requisitos
Authors: Barbosa Aline Ferreira , Lencastre Maria
Published: October 2024

A Engenharia de Requisitos envolve inúmeras interações sociais, que requerem do analista um alto nível de cooperação e empatia com pessoas de personalidades, valores e interesses diferentes. Nas equipes de desenvolvimento de software, independentemente do tamanho que seja o projeto, os conflitos fazem parte do seu ciclo de vida. Portanto, é importante o analista de requisitos monitorar continuamente os sinais que apontam a existência de conflitos, evitando o comprometimento do projeto.  Este artigo se concentra em identificar cenários de conflitos recorrentes nas equipes de desenvolvimento de software e utiliza uma estratégia para análise dos mesmos, a Comunicação Não Violenta (CNV). Foi realizado um estudo qualitativo utilizando como método de coleta uma entrevista semiestruturada com profissionais de 9 empresas distintas visando um aprofundamento nas situações de conflitos identificadas. Foram levantados um conjunto de cenários de conflito reais, assim como feita a análise dos mesmos, com base na CNV; isto ajudou os participantes (entrevistados) a observar o fato, independente de julgamentos, assim como identificar os sentimentos e necessidades presentes na situação; dessa forma, eles passaram a ter uma melhor compreensão do cenário onde ocorreu o conflito.
Métricas de Tamanho de Software com Métodos Ágeis no Setor Público: uma Revisão Sistemática
Authors: Mendonça Alexandre , Alencar Fernanda
Published: October 2024

A administrac~ao publica tem utilizado cada vez mais metodosageis, adequando-se a realidade do mercado. Muito embora continue obrigadaa mensurar suas entregas atraves de alguma metrica de tamanhode software, a escolha adequada dessa metrica pode denir o nvel desucesso dos projetos publicos. Neste artigo, identica-se as congurac~oesde metricas de tamanho de software em conjunto com metodos ageisno setor publico. Como instrumento metodologico para a identicac~aode evid^encias foi utilizada a revis~ao sistematica da literatura. A metricaPonto de Func~ao IFPUG e o metodo Manifesto Agil e Scrum foramidenticados como os mais utilizados no setor publico. A denic~ao decongurac~oes de uso de metricas e metodos ageis no setor publico tornapossvel direcionar a tomada de decis~oes para a conclus~ao com sucessodos projetos, no menor tempo possvel, com o menor custo aceitavel eentregando valor agregado perceptvel a sociedade.
Direcionadores para o Desenvolvimento Baseado em Modelos de Software Embarcado Aeronáutico
Authors: Sarkis André , Marques Johnny , Vieira Dias Luiz Alberto
Published: October 2024

O Desenvolvimento Baseado em Modelos (MBD, Model-Based Development) pode ser usado para especificar requisitos em vários níveis: produto, sistema, ou de software.  Na área de aviação, o uso de normas regulatórias no processo de certificação é usualmente requerido. A RTCA DO-178C e seus suplementos legislam sobre as necessidades que o processo de desenvolvimento de software precisa atender para tornar o produto de software certificável. Nos últimos anos, é notável o crescimento no uso de modelagem. Assim, o objetivo deste artigo é apresentar um conjunto de direcionadores para o MDB em Software Embarcado Aeronáutico, garantindo o atendimento às normas DO-178C e DO-331.  Além dos direcionadores, é apresentado um estudo de caso.
Pareamento de Nomes de Produtos e Serviços Utilizando Medidas de Similaridade Textual nos Níveis Alfabético, Léxico e Semântico
Authors: Meirelles Thiago Pereira , Gonçalves Eduardo Corrêa , Gomes Daniel Takata
Published: October 2024

O pareamento de textos é a tarefa de escolher, dentre um conjunto de textos possíveis, qual deles faz menção a um mesmo conceito ou objeto que outro determinado texto de entrada faz. Baseando-se em medidas de similaridade textual que atuam nos níveis alfabético, léxico e semântico, este trabalho compara a performance de estratégias automatizadas de pareamento que utilizam tais medidas de forma separada ou combinada. Essa performance foi avaliada através de experimento que consistiu no pareamento de descrições de produtos e serviços obtidos dos questionários de duas pesquisas do Instituto Brasileiro de Geografia e Estatística (IBGE): Pesquisa de Orçamentos Familiares (POF) e Índices de Preços do Consumidor (IPC). Em consonância com o observado em outros trabalhos, uma estratégia que combina medidas de similaridade diferentes, que atuam nos três níveis mencionados, obteve melhor performance, realizando um maior número de pareamentos corretos, quando comparada a estratégias que empregam apenas uma das medidas isoladamente. Uma investigação dos pareamentos incorretos produzidos pelas melhores estratégias foi feita com os objetivos de categorizar tipos de erros e propor abordagens adicionais que melhorem a acurácia.
Geodesic Convexity of graphs: partition and geodetic sets
Authors: Artigas Danilo , Dantas Simone , Dourado Mitre
Published: October 2024

This work describes the contribution of Artigas, Dantas, Dourado, and Szwarcfiter on the topic of convexity in the context of geodesic convex partitions, covers and geodetic sets from 2008 to 2013.
Jayme’s scientific contributions in the area of Convexity in Graphs
Authors: Coelho Erika , Dourado Mitre , Nascimento Julliano , Dos Santos Vinicius
Published: October 2024

We survey some of the contributions of Professor Jayme Luiz Szwarcfiter in the area of graph convexity, in celebration of his 80th birthday.
Why are they called Trivially Perfect Graphs?
Authors: Golumbic Martin Charles
Published: October 2024

Trivially perfect graphs are graphs for which the stability number equals the number of (maximal) cliques, for every induced subgraph. Trivially perfect graphs are equivalent to the {C_4, P_4}-free graphs, and to the comparability graphs orders whose Hasse diagram is a rooted tree. We survey classical and recent results on this fascinating and highly non-trivial graph family.
Interval Count of Interval Graphs
Authors: Oliveira Fabiano de Souza
Published: October 2024

The interval count problem is that of determining the smallest number of distinct interval lengths that is sufficient to represent an interval model of a given interval graph. The class of interval graphs is well known, with several applications. This article briefly summarizes my doctorate thesis done on the subject with supervision of Prof. Jayme Szwarcfiter, in his honor, on the occasion of his 80th birthday.
An exploratory study on the USARP method: improving the usability requirements elicitation and specification
Authors: Marques Anna Beatriz , Fiori Maria Victoria , Ferreira Bruna
Published: October 2024

USARP (USAbility Requirements with Personas and User stories) is a method for eliciting and specifying usability requirements using personas, user stories, and usability guidelines organized as cards. USARP suggests brainstorming sessions to discuss usability requirements oriented by its cards. We conducted an exploratory study in an academic environment to analyze the useof USARP in projects developed by undergraduate students acting as software engineers. We noted difficulties in selecting cards to use during the USARP adoption. Thus, this study proposes to evolve USARP to provide a more effective way to elicit and specify usability requirements. We reviewed the cards, removing redundant content and combining cards with similar content. Also, weproposed a checklist and a board to guide the selection of the cards according to users and system characteristics. Finally, the process suggested for adopting USARP was updated to reflect the use of the new artifacts. In this extended version, we provide an example of USARP in practice. We expect these improvements could guide the customization of the brainstorming sessions to be more effective and efficient.
Effects of Postmanufacture Conditioning on the Mechanical and Hygroscopic Properties of Extrusion Printed Wood–Sodium Silicate Composites
Authors: Alade Adefemi A. , Hematabadi Hojat , Carne Robert H. R. , Kukal Japneet , Fu Audrey Q. , McDonald Armando G. , Maughan Michael R. , Ibrahim Ahmed A. , Robertson Daniel J.
Published: October 2024

Additive manufacturing of wood–sodium silicate composites could aid in mitigating the carbon footprint of the building and construction industry. However, the effect of postmanufacture conditioning on the mechanical and physical properties of additively manufactured wood–sodium silicate composites is not well understood. This study investigated eight different postmanufacture drying processes, including: ambient indoor and outdoor conditions, oven-drying at two different temperatures, microwave drying, alcohol-induced dehydration using ethanol and denatured alcohol, and desiccant drying. Each postmanufacture conditioning treatment was assessed in terms of total moisture extraction and moisture extraction rate as well as the flexural strength, flexural stiffness, and hardness of the wood–sodium silicate samples after drying. In addition, the water absorption and volumetric swelling properties of the additively manufactured wood–sodium silicate samples were assessed via water submersion tests. The postmanufacture conditioning treatments were found to significantly affect the mechanical and physical properties of the samples. A universal ranking system was established based on cumulative rankings of each evaluated characteristic. Samples dried in ambient outdoor conditions achieved the best overall ranking and had the smallest carbon footprint. However, ovendried samples had the best flexural properties. Future studies investigating hybrid approaches in which composites are sequentially subjected to different drying methods will likely provide the most desirable mechanical and physical properties of wood–sodium silicate composites.
Addressing Group Composition in Adult Sex Offender Treatment for Improved Process and Completion Status
Authors: Frye Brenda M.
Published: October 2024

Abstract: The methods used to place individuals into treatment groups vary significantly, and the most effective group composition for the adult sex offender population has yet to be determined. This archival study analyzed group completion status based on group therapy composition to determine if homogeneous or heterogeneous groups led to improved retention, which has been demonstrated to reduce recidivism. Included in this archival study were 148 individuals referred to treatment as usual in a community-based program in the Midwest. Heterogeneous groups on underlying psychological issues contributing to sexual crime may be a preferable option for adult clients in sex offender treatment.
Caring for Creation in Julian of Norwich's Parable of the Lord and Servant
Authors: Killian Ann
Published: October 2024

Abstract: This essay expands upon the ecological implications of Julian's theology by arguing that her parable of the lord and servant exemplifies the call in Genesis 2:15 to cultivate and tend to Earth and all fleshly creatures. In conversation with present-day ecological theologies, I contend that Julian's example re-presents Genesis's theological claim that love of God is embodied by care for Earth and neighbor. When human persons are inhibited from laboring in the garden, they suffer from isolation and fall prey to despair. Julian's Revelation offers a spiritual resource to motivate ecological conversion, as Pope Francis urges in Laudato Si' .
Large language model-based optical network log analysis using LLaMA2 with instruction tuning
Authors: Pang Yue , Zhang Min , Liu Yanli , Li Xiangbin , Wang Yidi , Huan Yahang , Liu Zhuo , Li Jin , Wang Danshi
Published: October 2024

The optical network encompasses numerous devices and links, generating a significant volume of logs. Analyzing these logs is significant for network optimization, failure diagnosis, and health monitoring. However, the large-scale and diverse formats of optical network logs present several challenges, including the high cost and difficulty of manual processing, insufficient semantic understanding in existing analysis methods, and the strict requirements for data security and privacy. Generative artificial intelligence (GAI) with powerful language understanding and generation capabilities has the potential to address these challenges. Large language models (LLMs) as a concrete realization of GAI are well-suited for analyzing DCI logs, replacing human experts and enhancing accuracy. Additionally, LLMs enable intelligent interactions with network administrators, automating tasks and improving operational efficiency. Moreover, fine-tuning with open-source LLMs protects data privacy and enhances log analysis accuracy. Therefore, we introduce LLMs and propose a log analysis method with instruction tuning using LLaMA2 for log parsing, anomaly detection and classification, anomaly analysis, and report generation. Real log data extracted from the field-deployed network was used to design and construct instruction tuning datasets. We utilized the dataset for instruction tuning and demonstrated and evaluated the effectiveness of the proposed scheme. The results indicate that this scheme improves the performance of log analysis tasks, especially a 14% improvement in exact match rate for log parsing, a 13% improvement in F1-score for anomaly detection and classification, and a 23% improvement in usability for anomaly analysis, compared with the best baselines.
Domain adversarial adaptation framework for few-shot QoT estimation in optical networks
Authors: Cai Zhuojun , Wang Qihang , Deng Yubin , Zhang Peng , Zhou Gai , Li Yang , Khan Faisal Nadeem
Published: October 2024

The increasing complexity and dynamicity of future optical networks will necessitate accurate, fast, and low-cost quality-of-transmission (QoT) estimation. Machine learning-based QoT estimation models have shown promise in ensuring the reliability and efficiency of optical networks. However, the data-driven nature of these models impedes their application in practical settings. To address the problem of limited data availability in the target domain, known as the few-shot learning problem, we propose a domain adversarial adaptation method that aligns the distributions of representations from different source and target domains by minimizing the domain discrepancy quantified by the approximate Wasserstein distance. We demonstrate the method’s effectiveness through a theoretical proof and two example adaptations, i.e., from simulation to experimental data and from experimental to real network data. Our method consistently outperforms commonly used artificial neural networks (ANNs) and more advanced transfer learning approaches for various target domain data sizes. More profoundly, we show two ways to further improve the prediction accuracy, i.e., incorporating unlabeled target domain data in the training stage and utilizing the learned representations after training to train a new ANN with a reweighting strategy. In the adaptation to actual field data, our model, trained with only eight labeled network data samples, outperforms an ANN trained with 300 samples, thus reducing the labeled target domain data burden by more than 97%. The proposed method’s adaptability and generalizability make it a promising solution for accurate QoT estimation with low data requirements in future intelligent optical networks.
44-fs, 1-MHz, 70-µJ Yb-doped fiber laser system for high harmonic generation
Authors: Malekmohamadi Sedigheh , Pergament Mikhail , Kulcsar Gabor , Seidel Marcus , Liu Yizhou , Edelmann Marvin , Kellert Martin , Thesinga Jelto , Heyl Christoph M. , Kärtner Franz X.
Published: October 2024

We report the development of a robust Yb-doped fiber laser system based on chirped-pulse amplification (CPA), generating 44-fs laser pulses with up to 70-µJ pulse energy at a 1-MHz repetition rate. It consists of a Yb-doped nonlinear polarization evolution (NPE) mode-locked fiber oscillator, a chirped fiber Bragg grating (CFBG) stretcher, a wave-shaper for manipulating the spectrum of the signal, cascaded fiber amplifiers, and two compression units. The output pulse duration of 44 fs for efficient high harmonic generation (HHG) was achieved by a multi-pass multi-plate Herriott-type non-linear compression unit.
Atmospheric turbulence-distorted OAM mode recognition via multi-scale dilated convolution with multi-level feature fusion
Authors: Cao Xuguang , Wu Pengfei , Lei Sichen , Wang Jiao , Tan Zhenkun
Published: October 2024

Vortex beams with orbital angular momentum (OAM) significantly enhance system capacity, and high-precision recognition of OAM mode through atmospheric turbulence (AT) channels can markedly improve the information transmission capability of free-space optical communication systems. In this paper, with a cylindrical lens-assisted distinguish between positive and negative OAM, a reliable neural network combining multi-scale dilated convolution (MSDC) unit and multi-level feature fusion (MLFF) module is proposed to detect high order AT-distorted OAM modes. The network fully exploits the features in light-intensity images to achieve a highest recognition accuracy of 99.4% for mode-orders from -20 to +20 in a hybrid ATs dataset (C
n
2 = 5×10−16, 5×10−14, 5×10−12 m-2/3), and almost 96% even in strong turbulence. Experimental results on accuracy, efficiency, reliability, and robustness demonstrate that the proposed method excels and provides a trustworthy solution for complex AT-distorted OAM mode recognition.
Controlling spontaneous emission through the preparation of a photonic time-crystal
Authors: Lyubarov Mark , Dikopoltsev Alex , Segal Ohad , Plotnik Yonatan , Segev Mordechai
Published: October 2024

Photonic time crystals (PTCs) are materials whose dielectric permittivity is strongly modulated periodically in time at rates comparable to a single cycle of the waves propagating within. Such modulations can have a large impact on the propagation of waves in the medium. For example, all waves with wave vectors associated with the momentum gap are exponentially amplified, which in turn can lead to enhanced light-matter interaction. Here, we study the emission of radiation in a PTC and show that the power of the spontaneous radiation depends on the initial state of the field, and can be controlled through the turn-on process of the PTC. Specifically, if the PTC starts abruptly, the spontaneous emission rate grows monotonically towards the momentum gap, whereas if the PTC is turned on gradually the rate decreases towards the gap. This finding implies that the spontaneous emission rate can be designed and controlled by shaping the temporal modulation of the refractive index, a feature having major consequences for radiation generated in PTCs, such as PTC lasers and antennas.
Micro-cracks generation and growth manipulation by all-laser processing for low kerf-loss and high surface quality SiC slicing
Authors: Xiangfu Liu , Minghui Hong
Published: October 2024

Low kerf-loss and high surface quality silicon carbide (SiC) wafer slicing is key to reducing cost, improving productivity, and extending industrial applications. In this paper, a novel all-laser processing approach is proposed by combining laser micro-cracks generation and growth manipulation. The first high fluence pulsed laser is applied to generate micro-cracks inside SiC, which increases its laser energy absorption. The second low fluence pulsed laser achieves the manipulation of micro-cracks growth and interconnection to separate SiC wafer. The optimal laser processing parameters are obtained to separate a 4H-SiC substrate at a thickness of 500 µm. The sliced surface is clean with average surface roughness (Sa) of 186 nm, standard deviation of 0.037, and kerf-loss of 915 nm. This laser slicing approach can be applied for high-hardness transparent material separation.
Numerical investigation of steering synchronization dynamics of laterally coupled laser array with monolithically-integrated external cold cavity
Authors: Qi Jun , Lan Tian , Ma Wanli , Zhang Jinghao , Li Ying , Lou Yiwen , Qin Fengjiao , Liu Yu Ying , Wang Zhiyong
Published: October 2024

This study numerically explores the synchronization dynamics of a one-dimension edge-emitting laser array monolithically-integrated with an external cold cavity comprehensively, aiming to achieve an in-phase mode optical field. By employing the optical feedback rate equation, the impact of mutual feedback coefficient and coupling coefficient on the synchronization process are investigated thoroughly. The proposed external cold cavity, designed according to the Talbot effect, could significantly diminish the reflectivity of front facet through separated electrode structure, therefore facilitating the phase-locking process. Consequently, the study uncovers the effective regime for establishing in-phase mode operation. Additionally, the numerical analysis also reveals the vivid synchronization dynamic from a chaotic state to partially-phase-locked, then completely-phase-locked, and ultimately periodic oscillation. Furthermore, the impact of practical fabrication tolerances on the synchronization process are explored as well. Based on the simulation results, our work could offer valuable insights for steering the on-chip optical field and developing novel laser arrays with high beam quality.
Diode-pumped Kerr-lens mode-locked ytterbium-doped compositional mixed calcium aluminate laser
Authors: Li Zhi-Qiang , Lin Zhang-Lang , Zeng Huang-Jun , Nie Hai-Yu , Zhang Ge , Zhang Peixiong , Wu Wenjie , Chen Zhenqiang , Li Zhen , Loiko Pavel , Normani Simone , Mateos Xavier , Liang Hsing-Chih , Petrov Valentin , Chen Weidong
Published: October 2024

A diode-pumped Kerr-lens mode-locked laser generating 25 fs pulses at 1080 nm is demonstrated with an Yb3+-doped compositional mixed calcium aluminate crystal. The Yb:Ca(Gd,Y)AlO4 laser, which operates at a repetition rate of 65.6 MHz via soft-aperture Kerr-lens mode-locking, is pumped by a spatially single-mode, fiber-coupled diode laser. To the best of our knowledge, this is the first Kerr-lens mode-locked laser that utilizes an Yb3+-doped compositional mixed calcium aluminate crystal as the gain medium.
Digitally generated high-resolution mid-infrared dual-comb spectroscopy system based on electro-optic modulation
Authors: Yuan Zhengchao , Fan Xinyu , Xu Bingxin , Zhu Yidai , He Zuyuan
Published: October 2024

In this Letter, we propose a high-resolution dual-comb spectroscopy (DCS) in the mid-infrared (MIR) region. A broadband electro-optic frequency comb (EOFC) with a line spacing of 13 GHz is generated in the near-infrared region. The injection locking technique is employed to lock the distributed feedback (DFB) laser to each comb line of the 34 comb lines as the seed laser for the subsequent electro-optic modulation. A dual radio frequency (RF) comb source with a 50 MHz line spacing and a 13 GHz bandwidth drives a single IQ Mach–Zehnder modulator (IQ-MZM), functioning as a single-sideband (SSB) generator and producing a DCS with high spectrum flatness and resolution flexibility. The generated DCS is converted to the MIR region via a nonlinear difference frequency generation (DFG) system. A DCS with a bandwidth of 442 GHz and a resolution of 50 MHz is achieved in the 3.3 µm region, and the figure of merit reaches 2.94×106Hz12 in a 183.6 ms measurement time.
Femtosecond laser direct inscription of long period gratings in multicore fiber
Authors: Xu Mingjing , Ma Lin , Yu Fengrui , Zhao Yunhe , He Zuyuan
Published: October 2024

We demonstrate femtosecond laser direct writing long period gratings (LPGs) on multicore fibers (MCFs). By adopting the line-by-line inscription technique, LPGs can be independently fabricated at arbitrary cores of the MCF without removing the coating or altering fiber positions. Theoretical and experimental analyses were conducted to assess the laser energy distribution in the MCF and the impact of LPG parameters on filtering characteristics. LPGs inscribed in different cores under the same condition exhibited good spectral consistency, with a coupling efficiency of 90% (10 dB). Fabricated LPGs with various periods achieved multi-wavelength filtering effects in a single piece of the MCF with a widely adjustable wavelength range. The femtosecond laser direct inscription technique for fabricating spatial structures in the MCF demonstrates significant potential for space-division multiplexing (SDM) and wavelength-division multiplexing filtering applications.
Design of a broadband Si3N4 waveguide amplifier based on a gain medium of ion-sliced titanium-doped sapphire
Authors: Jiang Liying , Shen Shiji , Wei Ning , Wang Yan , He Jiajing , Dong Ningning , Xu Min , Hang Yin , Chen Jie , Wang Jun
Published: October 2024

In recent years, significant progress has been made in the on-chip integration of Ti:sapphire amplifiers and lasers, showing great potential in device miniaturization, cost reduction, and mass production. However, the further integration of such devices on standard CMOS platforms has been challenging due to its limits on the wafer bonding method between gain materials and substrates. Here, we present a novel, to the best of our knowledge, Si3N4 on-chip broadband optical waveguide amplifier scheme with an ultra-wide bandwidth of 650–900 nm and a peak gain of 28 dB based on an ion-sliced Ti:sapphire platform. The difficulty of heterogeneous integration is significantly reduced by growing Si3N4 thin films on Ti:sapphire. Moreover, by using homogeneous bonding combined with ion slicing technology, the target thickness of Ti:sapphire is expected to be easily controlled to less than 1 µm, greatly reducing the device volume and improving its practicality. Through subsequent experimental optimization, this work is expected to provide a new approach for the optimized design and experimental realization of on-chip Ti:sapphire waveguide amplifiers and lasers.