bluuebunny/crossref_metadata_2025 huggingface dataset:
Использование ПЦР-систем для диагностики возбудителей бактериоза черная ножка картофеля
Authors: Усков А.И. , Шмыгля И.В. , Стахеев А.А. , Завриев С.К. , Варицев Ю.А. , Галушка П.А. , Суслова Н.В.
Published: June 2024

Черная ножка картофеля – повсеместно распространенный в Российской Федерации бактериоз, вызываемый пектолитическими бактериями рода Pectobacterium из семейства Enterobacteriaceae. В 2009 г. на территории России были идентифицированы возбудители черной ножки картофеля, относящиеся к роду Dickeya: Dickeya dianthicola и Dickeya solani. Ежегодный недобор урожая из-за данной болезни может составлять от 1–2 до 50–70%. Основной путь распространения патогенных бактерий связан с перемещением семенного материала. Для выявления и идентификации фитопатогенов, вызывающих черную ножку картофеля, необходима разработка и оптимизация для практического использования высокочувствительных лабораторных методов. В 2019 г. в рамках Федеральной научно-технической программы (ФНТП) развития сельского хозяйства на 2017–2025 гг. Институтом биоорганической химии имени академиков М.М. Шемякина и Ю.А. Овчинникова РАН и Федеральным исследовательским центром картофеля имени А.Г. Лорха (ФИЦ картофеля) были разработаны новые тест-системы в формате ПЦР в реальном времени (ПЦР-РВ) для диагностики бактерий, вызывающих черную ножку картофеля, с аналитической чувствительностью выявления патогенов на уровне 10–50 копий плазмиды, содержащей специфический ПЦР-продукт. В статье представлены результаты сравнительных испытаний новых тест-систем для диагностики бактерий Pectobacterium atrosepticum, Dickeya dianthicola и Dickeya solani. При тестировании 20 сортообразцов семенного картофеля, поступивших в Испытательную лабораторию ФИЦ картофеля от производителей из 4 регионов Российской Федерации, в 15 случаях показано полное совпадение результатов анализа при использовании рутинных и новых испытуемых тест-систем.
Применение метода полимеразной цепной реакции для идентификации преимагинальных стадий Drosophila suzukii (Matsumura, 1931)
Authors: Колесникова Е.В. , Бондаренко Г.Н.
Published: June 2024

В процессе работы была изучена возможность применения метода полимеразной цепной реакции (ПЦР) определенных участков гена COI для идентификации азиатской ягодной дрозофилы Drosophila suzukii на преимагинальных стадиях развития и возможность применения изучаемых тестов для лабораторной диагностики. В статье приведены оригинальные данные (нуклеотидные последовательности) для идентификации целевого объекта методом ПЦР и их последующего использования в подборе видоспецифичных генетических маркеров.
Повилики естественных и антропогенно измененных сообществ Пензенской области и возможные биологические агенты их контроля
Authors: Сухолозова Е.А. , Сухолозов Е.А. , Сафонов А.В.
Published: June 2024

В статье представлены результаты видовой и фитосанитарной ревизии повилик Пензенской области. Установлено произрастание на территории региона 3 видов рода Cuscuta. Из них только повилика полевая – адвентивный вид, приуроченный исключительно к антропогенно измененным сообществам, в отличие от повилик европейской и хмелевидной, произрастающих в естественных пойменных фитоценозах. Представлены итоги изучения влияния представителей рода Smicronyx на повилики разных сообществ. Показана низкая значимость изученных долгоносиков как возможных биологических агентов контроля повилик.
ЛИЧНОСТНО-ОРИЕНТИРОВАННЫЙ ПОДХОД В ОБУЧЕНИИ АНГЛИЙСКОМУ ЯЗЫКУ
Authors: Назокат ФАЙЗУЛЛАЕВА
Published: June 2024

В этой статье анализируется адаптация личностно-ориентированного образования и исследуется, как преподаватели университетов внедрили его в преподавании второго языка с момента запуска образовательного сдвига, воплощенного в личностно-ориентированном образовании на военных уроках. Что еще более важно, анализ результатов качественного интервью обрисовывает «контекстуализированную» структуру, которая учитывает концептуальную природу глобальных предпосылок личностно-ориентированного образования, связывая их с восприятием и практикой учителей в конкретном контексте.
TARIXIY VOQELIK TASVIRIDA FAKT VA TALQIN MUAMMOSI (XURSHID DAVRON LIRIKASI MISOLIDA)
Authors: Ziyodaxon USMONOVA
Published: June 2024

Maqolada XX asr boshidagi qatag‘onlarga O‘zbekiston xalq shoiri Xurshid Davronning munosabati tarixiy faktlar asosida yoritilgan. Qayta qurish davridagi adabiy muhit, g‘oyaviy-badiiy yangilanishlar shoirning shu davrda yaratilgan she’rlari asosida tahlil qilingan.
USE OF THE PROJECT BASED LEARNING METHOD IN FOREIGN LANGUAGE LESSONS IN PRIMARY GRADES
Authors: Maçanova Cavahir
Published: June 2024

The purpose of this article is to review the features of the application of the project based learning method in the teaching of young students, and to state that the implementation of this learning method in primary classes is realistic and appropriate. Project based learning develops the student's social skills. This learning method allows the child to develop qualities such as morality and communication, develops creative skills, inculcates the ability to do useful work for society, and adapts the future generation to modern life. However, trends in the process of organizing project activities of young students indicate the need to adjust the resulting experience. Students deeply understand the new information they have learned, try to think valuable thoughts, establish dialogue and at the same time gain new knowledge.
AMNAP
Authors: Gil Izabel Castanha
Published: June 2024

A Associação dos Municípios da Nova Alta Paulista - AMNAP - constitui-se na principal representação política de trinta municípios localizados no extremo Oeste paulista. Procura-se resgatar os motivos que inspiraram a sua criação, em 1977, bem como sua trajetória marcada pela cooperação, competição e resistência dos líderes locais e regionais. A análise desses trinta anos de articulação política pode ser dividida em três momentos: de 1977 a 1982, de 1983 a 1996, e de 1997 até os dias atuais. Essa periodização foi estabelecida considerando-se as evidências de movimentação em cada momento, que refletiam e refletem a caracterização político-econômica estadual e nacional. As transformações contemporâneas impõem a necessidade de se refletir sobre o papel presente e futuro da entidade, adequando-se aos desafios regionais.
Caminhos verticais e colonização da Zona da Alta Paulista
Authors: Perli Fernando
Published: June 2024

Caminhos que cruzaram o espigão Peixe-Aguapeí, entre as décadas de 1910 e 1940, constituíram-se em estradas que interligaram povoados e cidades das regiões Noroeste e Alta Sorocabana, ambas localizadas no Oeste do Estado de São Paulo. Neste artigo, propomos analisar o papel destas rotas de ocupação no processo de colonização da Zona da Alta Paulista.
Leishmaniose visceral americana no município de Adamantina
Authors: Marinho César Antonio Franco
Published: June 2024

O artigo relata sobre um surto de Leishmaniose Visceral Americana no município de Adamantina e faz uma reflexão sobre a possibilidade de ocorrência de impactos ambientais e sua repercussão na saúde humana, mediante medidas de controle químico.
Prevalência de sinais e sintomas de DTM em acadêmicos e funcionários da FAI
Authors: Moreno Bruno Gonçalves Dias , Cardim Délcio , Gomes Natália Caroline Machado Coelho
Published: June 2024

As disfunções temporomandibulares (DTM) constituem um conjunto de sinais e sintomas que incluem ruídos articulares, cefaléias, bruxismo, dentre outros. De acordo com dados epidemiológicos acometem grande parte da população. O presente estudo teve como objetivo verificar a prevalência características de DTM, tais como sintomas, sensibilidade dolorosa dos músculos mastigatórios, presença de ruídos articulares e postura cervical em acadêmicos e funcionários das Faculdades Adamantinenses Integradas. Para esta pesquisa foram avaliados 50 indivíduos do sexo feminino selecionados aleatoriamente entre alunas e funcionárias da FAI, com idade entre 20 e 40 anos (24,6±4,5). A intensidade dos sintomas foi avaliada através de uma escala analógica visual de dor, a sensibilidade dolorosa por meio de palpação muscular, a avaliação da postura cervical foi realizada por inspeção em perfil. A postura cervical de cada paciente foi classificada como anteriorização, formando-se o Grupo 1; ou normal, formando o Grupo 2. A avaliação dos ruídos articulares foi realizada com um estetoscópio nas ATMs, durante o movimento de abertura da boca; dividindo as voluntárias em Grupo A, com estalido e Grupo B, sem estalido. A distribuição dos sintomas avaliados nas voluntárias deste estudo foram expressados através da freqüência relativa e foi analisada também a relação entre a presença do habito de bruxismo ou apertamento dos dentes e dor articular em indivíduos dos Grupos A e B, através do teste qui-quadrado. A intensidade dos sintomas foi comparada entre as voluntárias dos Grupos 1 e 2, e para todos os testes foram considerados significantes aqui valores de p<0,05. Os resultados mostraram que Acadêmicos e Funcionárias da FAI tiveram a cefaléia, cervicalgia e o bruxismo como os sintomas mais relatados. Não foi possível observar aqui relação entre anteriorização cervical e intensidade dos sintomas e há uma maior prevalência de dor articular e bruxismo nos pacientes que apresentam ruídos articulares. De acordo com estes resultados foi possível concluir que acadêmicos e Funcionárias da FAI apresentam várias das características clínicas comuns das DTM, os sintomas mais freqüentes foram cefaléia, cervicalgia e bruxismo ou apertamento, a presença de anteriorização cervical não interfere na intensidade dos sintomas e a dor articular e bruxismo/ apertamento parece estar diretamente relacionado como uma das causas do estalido articular.
Avaliação de cereais de inverno com e sem irrigação em Adamantina
Authors: Cavichioli José Carlos , Fagundes Jailson Lara , Nakayama Fernando Takayuki , Kasai Francisco Seiiti , Melo Marcelo Rosa
Published: June 2024

Avaliou-se o potencial produtivo de cinco variedades de triticale (X Tritico secale Wittmack), duas de cevada (Hordeum vulgare L.), quatro de trigo (Triticum aestivum L.) e uma de centeio (Secale cereale L.), em sistema de cultivo irrigado e não irrigado. O experimento foi instalado na Unidade Experimental do Pólo Regional de Desenvolvimento Tecnológico dos Agronegócios da Alta Paulista, em Adamantina, SP. Os resultados mostraram que a irrigação favoreceu a produtividade de fitomassa seca, a altura de plantas, a massa de 1000 grãos e o rendimento de grãos. O triticale IAC 2 destacou-se no rendimento de grãos e na produtividade de fitomassa seca total nos dois sistemas estudados. O cultivo de cereais de inverno mostrou-se viável na região de Adamantina, desde que irrigados.
Potencial hídrico foliar nos cafeeiros Obatã e Acaiá nas quatro estações do ano na região da Nova Alta Paulista (SP)
Authors: Nakayama Fernando Takayuki , Cavichioli José Carlos , Paulo Edison Martins , Kasai Francisco Seiiti , Sakai Emílio
Published: June 2024

O trabalho estudou, no ano agrícola 2002/03, no PRDTA da Alta Paulista, em Adamantina (SP), o potencial hídrico foliar dos cafeeiros e a umidade do solo sob as cultivares Acaiá e Obatã, nas populações de 2500 e 5000 plantas por hectare. Concluiu-se que o potencial hídrico foliar da população de 5000 plantas foi menor que o potencial da população de 2500 plantas por hectare, em cada estação do ano. O inverno foi a estação em que os cafeeiros mostraram os menores valores de potencial hídrico. A menor umidade no solo correspondeu à maior tensão de água na planta.
Sistemas de informação gerencial regional para micros, pequenas e médias empresas
Authors: Gabriel José Eduardo Ferreira
Published: June 2024

Os Sistemas de Informação Gerencial (SIG) são de grande importância para as empresas, pois permitem que sejam realizadas as integrações entre as diversas funções empresariais. Como exemplo, as funções compras, marketing, finanças, recursos humanos e produção passam a trocar informação, visando a alcançar maior competitividade. Nesse sentido, deverão ocorrer a otimização dos recursos, o cumprimento dos prazos, a redução dos custos associados, etc. Tipicamente, os Sistemas de Informação Gerencial possuem preço elevado, inviabilizando sua adoção pelas Micros, Pequenas e Médias Empresas (MPMEs). Este artigo apresenta a concepção de uma proposta de Sistema de Gestão Empresarial Regional direcionado às Micros, Pequenas e Médias Empresas na macro região da Nova Alta Paulista. Para tanto, se pretende adotar a plataforma www (World Wide Web – Internet), permitindo que essas empresas regionais transacionem as informações entre suas funções com um pequeno investimento. Dessa forma, as Micros, Pequenas e Médias Empresas terão maior competitividade para enfrentar os desafios do mercado, além da possibilidade de geração de novos postos de trabalho.
Statins as a possible factor affecting fluoroquinolone resistance of coagulase-negative Staphylococcus in the conjunctiva: a case-control study
Authors: Hong Yoo Rha , Oh Chi Eun , Lee Sang Joon
Published: June 2024

Background: Conjunctival bacterial flora is a common cause of endophthalmitis after ophthalmic procedures. This study investigated the conjunctival bacterial flora, especially coagulase-negative Staphylococcus (CoNS), and their antibiotic sensitivity in patients who underwent ophthalmic procedures. Factors related to fluoroquinolone resistance were also investigated.Methods: In total, 167 samples were analyzed from 135 patients who underwent cataract surgery or intravitreal injection at Kosin University Gospel Hospital between April 14, 2014, and September 29, 2016. Bacterial identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or VITEK 2 equipment. Antibiotic sensitivity tests were performed using an AST-P600 card with VITEK 2 equipment. Clinical information was extracted from patients’ medical records. Sixty-eight individuals with conjunctival flora containing CoNS were classified into the fluoroquinolone-sensitive and fluoroquinolone-resistant CoNS groups, and their characteristics were compared. Results: A total of 192 isolates of Gram-positive bacteria were identified, including Staphylococcus epidermidis (33.3%), Corynebacterium spp. (18.8%), and CoNS other than S. epidermidis (9.2%). Of the 106 CoNS isolates, 68.9%, 69.8%, and 58.5% were sensitive to ciprofloxacin, levofloxacin, and norfloxacin, respectively. In patients with CoNS, statin use within 3 months before sample collection was significantly associated with fluoroquinolone resistance (p=0.016). Statin use was a significant risk factor for fluoroquinolone resistance in multivariate logistic regression analysis (odds ratio, 4.86; 95% confidence interval, 1.25–18.91; p=0.022).Conclusions: CoNS, including S. epidermidis, was the most common conjunctival bacterial flora, with a fluoroquinolone sensitivity rate ranging from 58.5% to 69.8% in patients undergoing ophthalmic procedures. Statin use was a significant risk factor for fluoroquinolone resistance.
Repenser le travail social au Québec : comment intégrer les préoccupations environnementales dans la pratique ?
Authors: MacDonald Sue-Ann , Rioux Érick , Carlton Rosemary , Dominelli Lena , Khoury Emmanuelle
Published: June 2024

Au Québec, les liens entre la pratique du travail social et la crise écologique, ainsi que les impacts de celle-ci sur les populations en situation de vulnérabilité, sont des avenues qui commencent à être explorées dans la recherche. Cet article s’inscrit dans ce mouvement et expose notre analyse issue d’un projet de recherche exploratoire auprès de praticiennes en travail social. Il sera question d’examiner leurs points de vue sur les connexions qu’elles établissent entre leur pratique et l’écologie. Notre analyse montre que les participantes reconnaissent la pertinence de leur profession face à la crise écologique, mais que leur contexte de pratique ainsi que la façon dont l’environnement et la nature sont conceptualisés à même la profession peuvent être des facteurs contraignants pour l’écologisation du travail social. Cet article s’inscrit donc dans une invitation collective à réfléchir au travail social d’aujourd’hui et de demain devant la nécessité d’intégrer de manière plus significative les préoccupations environnementales dans la pratique professionnelle.
De la fin du stage à la suite du monde : un plaidoyer collectif pour le renouvellement
de la formation en travail social dans un contexte de crises socio-écologiques
Authors: Larocque Emmanuelle , Pinsonneault Natalie , Soucy Pierre-Olivier , Sauvagnat Virginie , Erdinç Seline , Matte Isabelle , Kingsley Pascale
Published: June 2024

Confronté à de nouveaux problèmes socioécologiques d’envergure qui touchent
toutes les sphères de l’intervention, le travail social est appelé à renouveler son cursus
académique. Ce récit de pratique vise à contribuer à la réflexion, déjà entamée, sur les
types d’activités pédagogiques qui s’alignent sur les objectifs transformatifs du travail
écosocial. L’article présente un document collectif rédigé par six personnes étudiantes de
premier cycle en travail social dans le cadre d’un cours d’intégration des expériences de
stage, interrompu par la pandémie de COVID-19. Il s’agit d’une activité pédagogique qui a
été pensée lors de la reconfiguration des modalités de réussite du stage en raison du
basculement des cours universitaires en ligne en mars 2020. Le but de cet exercice était
d’offrir un espace de partage afin que les personnes étudiantes puissent extérioriser leurs
inquiétudes du moment, mais aussi pour co-construire et renégocier les frontières du travail
social au regard de la complexité des crises sanitaires et écologiques. S’appuyant sur le
modèle conceptuel écosocial, l’article positionne l’action collective comme moyen de
favoriser une prise de parole collective et inclusive des jeunes au sein des espaces
académiques. La méthodologie utilisée pour créer et diffuser le document collectif est
développée et appuyée par des extraits du document final. Les retombées seront ensuite
discutées selon les points de vue des personnes étudiantes et de la professeure. Ces regards
croisés permettront d’identifier des pistes d’action pour la pédagogie écosociale, tout en
posant la prémisse qu’un tournant expérientiel et collectif s’avère nécessaire pour
développer des pratiques porteuses d’espoir et de transformation
socioécologique.
Les facteurs influençant la profondeur de traitement de la rétroaction corrective écrite des apprenants de français langue étrangère
Authors: Lira-Gonzales Maria-Lourdes , Nassaji Hossein , Chao Chao Kuok Wa
Published: June 2024

La rétroaction corrective écrite (RCE) est un domaine qui suscite l’attention des chercheurs en langue seconde (L2), que ce soit sur le plan pédagogique ou théorique (Lira-Gonzales et Nassaji, 2020). Il existe un consensus sur ses bénéfices dans l’apprentissage d’une langue étrangère/L2, mais très peu de recherches ont examiné la manière dont les apprenants traitent les différents types de rétroaction. À partir d’une approche mixte, cet article examine la façon dont les apprenants du français langue étrangère (FLE) analysent cognitivement deux types de rétroaction corrective (RC) : indirecte (avec des codes) et directe (correction fournie). Seize étudiants d’un cours d’écriture en FLE d’une université publique costaricaine y ont participé pendant le premier semestre de 2021. Les questions suivantes ont guidé cette recherche : (1) Les types de rétroaction peuvent-ils influencer la profondeur de traitement (PdT) de la RC de l’apprenant ? (2) Les types d’erreurs peuvent-ils influencer la PdT de la RC de l’apprenant ? La collecte de données était basée sur deux textes argumentatifs (d’environ 500 mots chacun) rédigés pendant le semestre et sur une réflexion à haute voix après chaque activité d’écriture. Les participants ont reçu de la RC indirecte pour le premier texte et de la RC directe pour le deuxième. Les résultats ont démontré qu’il n’y avait pas de relation significative entre le type de rétroaction et la PdT des informations des apprenants. Cependant, il existait une relation significative entre la PdT et certains types d’erreurs morphologiques, comme les accords.
Semaine de travail de quatre jours : quels sont les impacts sur les travailleurs ?
Authors: Samson Irène , Lallier-Beaudoin Marie-Claude , Courtemanche Jeanne , Girard Julie-Andrée
Published: June 2024

Depuis de nombreuses années, à travers les pays industrialisés, les organisations de tous les secteurs cherchent des stratégies pour améliorer leur productivité ainsi que la qualité de leur environnement de travail. Ce défi a d’ailleurs été amplifié par la pandémie reliée au coronavirus COVID-19 (Fontinha, 2021). Cette nouvelle réalité a amené les organisations à se réinventer pour demeurer compétitives. Parmi les solutions considérées, la semaine de travail de quatre jours retient l’attention des organisations et de la communauté scientifique (Sng et al., 2021). Or, malgré l’aspect prometteur de ce modèle et une poignée d’études sur le sujet, il semble difficile d'obtenir un aperçu clair de ses retombées sur les travailleurs en raison d'un état de la documentation épars et fragmenté. À la lumière de cette situation, la présente étude vise à brosser un portrait des diverses retombées individuelles connues jusqu’à présent de cette modalité de travail. Pour ce faire, la présente recherche s’appuie sur la méthode en cinq étapes de la scoping study, proposée par Arksey et O’Malley (2005) : (1) définition de la question de recherche ; (2) identification des données documentaires pertinentes ; (3) sélection des données documentaires ; (4) classification des données ; (5) analyse, synthèse et présentation des résultats. Sur un potentiel de 2183 écrits, 22 écrits empiriques, théoriques et pratiques ont été compilés et analysés. De cette analyse, cinq grandes catégories regroupant à la fois des retombées positives et négatives ont été dégagées : la productivité, la santé psychologique, l’interface travail-vie personnelle, les relations interpersonnelles et la satisfaction générale. En plus de sensibiliser les organisations aux effets de cette nouvelle alternative de travail, cette étude offre des pistes intéressantes de recherche et d’action aux chercheurs et praticiens désirant maximiser les effets positifs de cette modalité de travail prometteuse.
Ultracold atomic imaging based on enhanced fringe removal method
Authors: Wang Shuai , Li Xi , Yao Xing-Can ,   Hefei National Research Center for Physical Sciences at the Microscale, School of Physical Sciences, University of Science and Technology of China, Hefei 230026, China,   Shanghai Research Center for Quantum Sciences, CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Shanghai 201315, China,   Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
Published: June 2024

Absorption imaging is the foundation for quantitative measurements in experiments on ultracold atoms. This technique mainly involves capturing images of both the probing light field and the atom absorption light field. In this process, the unavoidable jitter of the probing light introduces imaging noise of fringe patterns into the atomic optical density distribution OD. In conventional fringe removal algorithms, this type of noise can be normalized by constructing an optimal reference image from multiple reference images that have been actually taken, which shares similar fringe patterns to an absorption image (Fig. (a)). Although this method works well in the region without atomic signal, they often overlook the modulation of the noise signal due to atomic absorption effects, leading to persistent residual fringes on the atom clouds. This problem becomes more pronounced with atomic density increasing. Here, we propose an enhanced fringe removal algorithm that takes into account the effects of atomic absorption, and actively modulates the intensity of the noise signal in the reference image constructed by conventional fringe removal algorithms (Fig. (b)), effectively preventing the residual fringes from forming, thus significantly improving the signal-to-noise ratio of the atomic images. When applied to the absorption imaging of homogeneous Fermi gases with high density, as shown in Fig. (d), this new algorithm successfully reduces the relative standard deviation of optical depth characterizing atomic density fluctuations by approximately 37%, which is about 3 times the relative standard deviation by conventional algorithm. Three subgraphs in Fig. (e) show the optical depth distribution at corresponding data points labeled by square boxes in Fig. (d). Furthermore, we also use this technique to quantitatively determine the second sound in the unitary Fermi superfluid of 6Li atoms. Compared with conventional fringe removal methods, our new algorithm increases the correlation function’s contrast of the density wave nearly 4 times, therefore enhancing the intensity of the density response spectrum by approximately 15% with half the measured standard error, paving the way for quantitatively determining the speed and attenuation of the second sound. These results demonstrate that the enhanced fringe removal algorithm not only effectively suppresses fringe noise, but also facilitates the identification and detection of important physical phenomena in high-density atomic systems, such as some collective excitations and new quantum phases.
Partitioning to ordered membrane domains regulates the kinetics of secretory traffic
Authors: Castello-Serrano Ivan , Heberle Frederick A , Diaz-Rohrer Barbara , Ippolito Rossana , Shurer Carolyn R , Lujan Pablo , Campelo Felix , Levental Kandice R , Levental Ilya
Published: June 2024

The organelles of eukaryotic cells maintain distinct protein and lipid compositions required for their specific functions. The mechanisms by which many of these components are sorted to their specific locations remain unknown. While some motifs mediating subcellular protein localization have been identified, many membrane proteins and most membrane lipids lack known sorting determinants. A putative mechanism for sorting of membrane components is based on membrane domains known as lipid rafts, which are laterally segregated nanoscopic assemblies of specific lipids and proteins. To assess the role of such domains in the secretory pathway, we applied a robust tool for synchronized secretory protein traffic (RUSH, Retention Using Selective Hooks) to protein constructs with defined affinity for raft phases. These constructs consist solely of single-pass transmembrane domains (TMDs) and, lacking other sorting determinants, constitute probes for membrane domain-mediated trafficking. We find that while raft affinity can be sufficient for steady-state PM localization, it is not sufficient for rapid exit from the endoplasmic reticulum (ER), which is instead mediated by a short cytosolic peptide motif. In contrast, we find that Golgi exit kinetics are highly dependent on raft affinity, with raft preferring probes exiting the Golgi ~2.5-fold faster than probes with minimal raft affinity. We rationalize these observations with a kinetic model of secretory trafficking, wherein Golgi export can be facilitated by protein association with raft domains. These observations support a role for raft-like membrane domains in the secretory pathway and establish an experimental paradigm for dissecting its underlying machinery.
Factorized visual representations in the primate visual system and deep neural networks
Authors: Lindsey Jack W. , Issa Elias B.
Published: June 2024

Object classification has been proposed as a principal objective of the primate ventral visual stream and has been used as an optimization target for deep neural network models (DNNs) of the visual system. However, visual brain areas represent many different types of information, and optimizing for classification of object identity alone does not constrain how other information may be encoded in visual representations. Information about different scene parameters may be discarded altogether (“invariance”), represented in non-interfering subspaces of population activity (“factorization”) or encoded in an entangled fashion. In this work, we provide evidence that factorization is a normative principle of biological visual representations. In the monkey ventral visual hierarchy, we found that factorization of object pose and background information from object identity increased in higher-level regions and strongly contributed to improving object identity decoding performance. We then conducted a large-scale analysis of factorization of individual scene parameters – lighting, background, camera viewpoint, and object pose – in a diverse library of DNN models of the visual system. Models which best matched neural, fMRI and behavioral data from both monkeys and humans across 12 datasets tended to be those which factorized scene parameters most strongly. Notably, invariance to these parameters was not as consistently associated with matches to neural and behavioral data, suggesting that maintaining non-class information in factorized activity subspaces is often preferred to dropping it altogether. Thus, we propose that factorization of visual scene information is a widely used strategy in brains and DNN models thereof.
A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery
Authors: Liu Zhuang , Gillis Thomas G , Raman Srivatsan , Cui Qiang
Published: June 2024

New experimental findings continue to challenge our understanding of protein allostery. Recent deep mutational scanning study showed that allosteric hotspots in the tetracycline repressor (TetR) and its homologous transcriptional factors are broadly distributed rather than spanning well-defined structural pathways as often assumed. Moreover, hotspot mutation-induced allostery loss was rescued by distributed additional mutations in a degenerate fashion. Here, we develop a two-domain thermodynamic model for TetR, which readily rationalizes these intriguing observations. The model accurately captures the in vivo activities of various mutants with changes in physically transparent parameters, allowing the data-based quantification of mutational effects using statistical inference. Our analysis reveals the intrinsic connection of intra- and inter-domain properties for allosteric regulation and illustrate epistatic interactions that are consistent with structural features of the protein. The insights gained from this study into the nature of two-domain allostery are expected to have broader implications for other multi-domain allosteric proteins.
Spectral decomposition unlocks ascidian morphogenesis
Authors: Dokmegang Joel , Faure Emmanuel , Lemaire Patrick , Munro Ed , Mani Madhav
Published: June 2024

Describing morphogenesis generally consists in aggregating the multiple high resolution spatiotemporal processes involved into reproducible low dimensional morphological processes consistent across individuals of the same species or group. In order to achieve this goal, biologists often have to submit movies issued from live imaging of developing embryos either to a qualitative analysis or to basic statistical analysis. These approaches, however, present noticeable drawbacks, as they can be time consuming, hence unfit for scale, and often lack standardisation and a firm foundation. In this work, we leverage the power of a continuum mechanics approach and flexibility of spectral decompositions to propose a standardised framework for automatic detection and timing of morphological processes. First, we quantify whole-embryo scale shape changes in developing ascidian embryos by statistically estimating the strain-rate tensor field of its time-evolving surface without the requirement of cellular segmentation and tracking. We then apply to this data spectral decomposition in space using spherical harmonics and in time using wavelets transforms. These transformations result in the identification of the principal dynamical modes of ascidian embryogenesis and the automatic unveiling of its blueprint in the form of spectograms that tell the story of development in ascidian embryos.
Speech and music recruit frequency-specific distributed and overlapping cortical networks
Authors: te Rietmolen Noémie , Mercier Manuel , Trébuchon Agnès , Morillon Benjamin , Schön Daniele
Published: June 2024

To what extent does speech and music processing rely on domain-specific and domain-general neural networks? Using whole-brain intracranial EEG recordings in 18 epilepsy patients listening to natural, continuous speech or music, we investigated the presence of frequency-specific and network-level brain activity. We combined it with a statistical approach in which a clear operational distinction is made between
shared
,
preferred,
and domain-
selective
neural responses. We show that the majority of focal and network-level neural activity is shared between speech and music processing. Our data also reveal an absence of anatomical regional selectivity. Instead, domain-selective neural responses are restricted to distributed and frequency-specific coherent oscillations, typical of spectral fingerprints. Our work highlights the importance of considering natural stimuli and brain dynamics in their full complexity to map cognitive and brain functions.
Emerging role of oncogenic β-catenin in exosome biogenesis as a driver of immune escape in hepatocellular carcinoma
Authors: Dantzer Camille , Vaché Justine , Brunel Aude , Mahouche Isabelle , Raymond Anne-Aurélie , Dupuy Jean-William , Petrel Melina , Bioulac-Sage Paulette , Perrais David , Dugot-Senant Nathalie , Verdier Mireille , Bessette Barbara , Billottet Clotilde , Moreau Violaine
Published: June 2024

Immune checkpoint inhibitors have produced encouraging results in cancer patients. However, the majority of β-catenin-mutated tumors have been described as lacking immune infiltrates and resistant to immunotherapy. The mechanisms by which oncogenic β-catenin affects immune surveillance remain unclear. Herein, we highlighted the involvement of β-catenin in the regulation of the exosomal pathway and, by extension, in immune/cancer cell communication in hepatocellular carcinoma (HCC). We showed that mutated β-catenin represses expression of
SDC4
and
RAB27A
, two main actors in exosome biogenesis, in both liver cancer cell lines and HCC patient samples. Using nanoparticle tracking analysis and live-cell imaging, we further demonstrated that activated β-catenin represses exosome release. Then, we demonstrated in 3D spheroid models that activation of β-catenin promotes a decrease in immune cell infiltration through a defect in exosome secretion. Taken together, our results provide the first evidence that oncogenic β-catenin plays a key role in exosome biogenesis. Our study gives new insight into the impact of β-catenin mutations on tumor microenvironment remodeling, which could lead to the development of new strategies to enhance immunotherapeutic response.
Bacterial exonuclease III expands its enzymatic activities on single-stranded DNA
Authors: Wang Hao , Ye Chen , Lu Qi , Jiang Zhijie , Jiang Chao , Zhou Chun , Li Na , Zhang Caiqiao , Zhao Guoping , Yue Min , Li Yan
Published: June 2024

Bacterial exonuclease III (ExoIII), widely acknowledged for specifically targeting double-stranded DNA (dsDNA), has been documented as a DNA repair-associated nuclease with apurinic/apyrimidinic (AP)-endonuclease and 3′→5′ exonuclease activities. Due to these enzymatic properties, ExoIII has been broadly applied in molecular biosensors. Here, we demonstrate that ExoIII (
Escherichia coli
) possesses highly active enzymatic activities on ssDNA. By using a range of ssDNA fluorescence-quenching reporters and fluorophore-labelled probes coupled with mass spectrometry analysis, we found ExoIII cleaved the ssDNA at 5′-bond of phosphodiester from 3′ to 5′ end by both exonuclease and endonuclease activities. Additional point mutation analysis identified the critical residues for the ssDNase action of ExoIII and suggested the activity shared the same active center with the dsDNA-targeted activities of ExoIII. Notably, ExoIII could also digest the dsDNA structures containing 3′-end ssDNA. Considering most ExoIII-assisted molecular biosensors require the involvement of single-stranded DNA (ssDNA) or nucleic acid aptamer containing ssDNA, the activity will lead to low efficiency or false positive outcome. Our study revealed the multi-enzymatic activity and the underlying molecular mechanism of ExoIII on ssDNA, illuminating novel insights for understanding its biological roles in DNA repair and the rational design of ExoIII-ssDNA involved diagnostics.
Does bumblebee preference of continuous over interrupted strings in string-pulling tasks indicate means-end comprehension?
Authors: Wen Chao , Lu Yuyi , Solvi Cwyn , Dong Shunping , Wang Cai , Wen Xiujun , Xiao Haijun , Dong Shikui , Wen Junbao , Peng Fei , Chittka Lars
Published: June 2024

Bumblebees (Bombus terrestris) have been shown to engage in string-pulling behavior to access rewards. The objective of this study was to elucidate whether bumblebees display means-end comprehension in a string-pulling task. We presented bumblebees with two options: one where a string was connected to an artificial flower containing a reward and the other presenting an interrupted string. Bumblebees displayed a consistent preference for pulling connected strings over interrupted ones after training with a stepwise pulling technique. When exposed to novel string colors, bees continued to exhibit a bias towards pulling the connected string. This suggests that bumblebees engage in featural generalization of the visual display of the string connected to the flower in this task. If the view of the string connected to the flower was restricted during the training phase, the proportion of bumblebees choosing the connected strings significantly decreased. Similarly, when the bumblebees were confronted with coiled connected strings during the testing phase, they failed to identify and reject the interrupted strings. This finding underscores the significance of visual consistency in enabling the bumblebees to perform the task successfully. Our results suggest that bumblebees’ ability to distinguish between continuous strings and interrupted strings relies on a combination of image matching and associative learning, rather than means-end understanding. These insights contribute to a deeper understanding of the cognitive processes employed by bumblebees when tackling complex spatial tasks.
A robust brain network for sustained attention from adolescence to adulthood that predicts later substance use
Authors: Weng Yihe , Kruschwitz Johann , Rueda-Delgado Laura M , Ruddy Kathy L , Boyle Rory , Franzen Luisa , Serin Emin , Nweze Tochukwu , Hanson Jamie , Smyth Alannah , Farnan Tom , Banaschewski Tobias , Bokde Arun LW , Desrivières Sylvane , Flor Herta , Grigis Antoine , Garavan Hugh , Gowland Penny A , Heinz Andreas , Brühl Rüdiger , Martinot Jean-Luc , Martinot Marie-Laure Paillère , Artiges Eric , McGrath Jane , Nees Frauke , Papadopoulos Orfanos Dimitri , Paus Tomas , Poustka Luise , Holz Nathalie , Fröhner Juliane , Smolka Michael N , Vaidya Nilakshi , Schumann Gunter , Walter Henrik , Whelan Robert ,   IMAGEN Consortium
Published: June 2024

Substance use, including cigarettes and cannabis, is associated with poorer sustained attention in late adolescence and early adulthood. Previous studies were predominantly cross-sectional or under-powered and could not indicate if impairment in sustained attention was a predictor of substance use or a marker of the inclination to engage in such behavior. This study explored the relationship between sustained attention and substance use across a longitudinal span from ages 14 to 23 in over 1000 participants. Behaviors and brain connectivity associated with diminished sustained attention at age 14 predicted subsequent increases in cannabis and cigarette smoking, establishing sustained attention as a robust biomarker for vulnerability to substance use. Individual differences in network strength relevant to sustained attention were preserved across developmental stages and sustained attention networks generalized to participants in an external dataset. In summary, brain networks of sustained attention are robust, consistent, and able to predict aspects of later substance use.
A robust brain network for sustained attention from adolescence to adulthood that predicts later substance use
Authors: Weng Yihe , Kruschwitz Johann , Rueda-Delgado Laura M. , Ruddy Kathy , Boyle Rory , Franzen Luisa , Serin Emin , Nweze Tochukwu , Hanson Jamie , Smyth Alannah , Farnan Tom , Banaschewski Tobias , Bokde Arun L.W. , Desrivières Sylvane , Flor Herta , Grigis Antoine , Garavan Hugh , Gowland Penny , Heinz Andreas , Brühl Rüdiger , Martinot Jean-Luc , Martinot Marie-Laure Paillère , Artiges Eric , McGrath Jane , Nees Frauke , Orfanos Dimitri Papadopoulos , Paus Tomáš , Poustka Luise , Holz Nathalie , Fröhner Juliane H. , Smolka Michael N. , Vaidya Nilakshi , Schumann Gunter , Walter Henrik , Whelan Robert ,   IMAGEN Consortium
Published: June 2024

Substance use, including cigarettes and cannabis, is associated with poorer sustained attention in late adolescence and early adulthood. Previous studies were predominantly cross-sectional or under-powered and could not indicate if impairment in sustained attention was a consequence of substance-use or a marker of the inclination to engage in such behaviour. This study explored the relationship between sustained attention and substance use across a longitudinal span from ages 14 to 23 in over 1,000 participants. Behaviours and brain connectivity associated with diminished sustained attention at age 14 predicted subsequent increases in cannabis and cigarette smoking, establishing sustained attention as a robust biomarker for vulnerability to substance use. Individual differences in network strength relevant to sustained attention were preserved across developmental stages and sustained attention networks generalized to participants in an external dataset. In summary, brain networks of sustained attention are robust, consistent, and able to predict aspects of later substance use.
Mechanical forces pattern endocardial Notch activation via mTORC2-PKC pathway
Authors: Mu Yunfei , Hu Shijia , Liu Xiangyang , Tang Xin , Lin Jiayi , Shi Hongjun
Published: June 2024

Notch signaling has been identified as a key regulatory pathway in patterning the endocardium through activation of endothelial-to-mesenchymal transition (EMT) in the atrioventricular canal (AVC) and proximal outflow tract (OFT) region. However, the precise mechanism underlying Notch activation remains elusive. By transiently blocking the heartbeat of E9.5 mouse embryos, we found that Notch activation in the arterial endothelium was dependent on its ligand Dll4, whereas the reduced expression of Dll4 in the endocardium led to a ligand-depleted field, enabling Notch to be specifically activated in AVC and OFT by regional increased shear stress. The strong shear stress altered the membrane lipid microdomain structure of endocardial cells, which activated mTORC2 and PKC and promoted Notch1 cleavage even in the absence of strong ligand stimulation. These findings highlight the role of mechanical forces as a primary cue for endocardial patterning and provide insights into the mechanisms underlying congenital heart diseases of endocardial origin.
The autophagy protein, ATG14 safeguards against unscheduled pyroptosis activation to enable embryo transport during early pregnancy
Authors: Popli Pooja , Oestreich Arin K. , Maurya Vineet K. , Rowen Marina N. , Masand Ramya , Holtzman Michael J. , Zhang Yong , Lydon John , Akira Shizuo , Moley Kelle H. , Kommagani Ramakrishna
Published: June 2024

Recurrent pregnancy loss (RPL), characterized by two or more failed clinical pregnancies, poses a significant challenge to reproductive health. In addition to embryo quality and endometrial function, proper oviduct function is also essential for successful pregnancy establishment. Therefore, structural abnormalities or inflammation resulting from infection in the oviduct may impede the transport of embryos to the endometrium, thereby increasing the risk of miscarriage. However, the precise cellular mechanisms that maintain the structural and functional integrity of the oviduct are not studied yet. Here, we report that autophagy is critical for maintaining the oviduct homeostasis and keeping the inflammation under check to enable embryo transport. Specifically, the loss of the autophagy-related gene,
Atg14
in the oviduct causes severe structural abnormalities compromising its cellular plasticity and integrity leading to the retention of embryos. Interestingly, the selective loss of
Atg14
in oviduct ciliary epithelial cells did not impact female fertility, highlighting the specificity of ATG14 function in distinct cell types within the oviduct. Mechanistically, loss of
Atg14
triggered unscheduled pyroptosis leading to inappropriate embryo retention and impeded embryo transport in the oviduct. Finally, pharmacological activation of pyroptosis in pregnant mice led to an impairment in embryo transport. Together, we found that ATG14 safeguards against unscheduled pyroptosis activation to enable embryo transport from the oviduct to uterus for the successful implantation. Of clinical significance, these findings provide possible insights on the underlying mechanism(s) of early pregnancy loss and might aid in developing novel prevention strategies using autophagy modulators.
Compressed sensing based approach identifies modular neural circuitry driving learned pathogen avoidance
Authors: Hallacy Timothy , Ringstad Niels , Ramanathan Sharad
Published: June 2024

An animal’s survival hinges on its ability to integrate past information to modify future behavior. The nematode
C. elegans
adapts its behavior based on prior experiences with pathogen exposure, transitioning from attraction to avoidance of the pathogen. A systematic screen for the neural circuits that integrate the information of previous pathogen exposure to modify behavior has not been feasible because of the lack of tools for neuron type specific perturbations. We overcame this challenge using methods based on compressed sensing to efficiently determine the roles of individual neuron types in learned avoidance behavior. Our screen revealed that distinct sets of neurons drive exit from lawns of pathogenic bacteria and prevent lawn re-entry. Using calcium imaging of freely behaving animals and optogenetic perturbations, we determined the neural dynamics that regulate one key behavioral transition after infection: stalled re-entry into bacterial lawns. We find that key neuron types govern pathogen lawn specific stalling but allow the animal to enter nonpathogenic
E. coli
lawns. Our study shows that learned pathogen avoidance requires coordinated transitions in discrete neural circuits and reveals the modular structure of this complex adaptive behavioral response to infection.