Entire Repertoire Research Articles

Examining the use of bilingual accommodations in digital math assessments: User perceptions

Digital math assessments with bilingual accommodations allow multilingual learners to use their entire linguistic repertoire to showcase their knowledge and skills. The bilingual accommodations, which include tools like language translation and audio prompts in both English and Spanish, are designed to be adaptable, giving multilingual learners the freedom to view or listen to the items in either language and to write or say their responses in either language or a combination of both. This study examined how 56 middle school emergent bilingual learners used these bilingual accommodations and explored the perceptions of teachers and students regarding these accommodations. This study provides evidence regarding using bilingual accommodation in math assessments for middle school emergent multilingual learners. The results showed how students used their full linguistic repertoire and language modalities to showcase their math knowledge and skills. Both teachers and students reported having positive perceptions of the bilingual accommodations, reinforcing its responsiveness to different learners’ needs and preferences.

Family language policy: the impact of multilingual experiences at university and language practices at home

ABSTRACT This article presents the findings from a study that explored how the language practices and management to which 156 students from universities in China reported being exposed at home, alongside their language beliefs, use of their entire linguistic repertoire when reading, listening, speaking, and writing at university, and emotions related to being multilingual predicted the language practices and management they envisioned for their own families. Data were gathered through a comprehensive questionnaire administered on campus. The results revealed that the more participants reported exposure to multilingual language practices at home and the stronger their beliefs in the benefits of a multilingual upbringing, the more determined they were to implement multilingual language practices with their own families. Moreover, using languages fluidly at university correlated positively with participants’ desire to adopt a more conscious approach to language management in their future families.

Reading Practices with Multilingual Children in Norwegian Kindergartens

One in five children in Norwegian kindergartens are multilingual, and reading practices that encourage the use of multilinguals’ entire linguistic repertoire can serve as important opportunities for language sharing, which is also encouraged by the Norwegian education authorities. In this study, we initially aimed to explore kindergarten reading practices involving languages other than Norwegian. When it became clear that such practices are rare, we expanded our investigation to include early childhood teachers’ experiences of reading with multilingual children more broadly. Our data sources consist of both self-reported data from a nationwide survey on reading practices in Norwegian kindergartens and six semi-structured focus group interviews with kindergarten staff. As reading in Norwegian kindergartens appears to occur in a space between kindergarten children’s right to meaningful experiences in different languages and their need to learn Norwegian, we shed light on what early childhood teachers highlight as central resources for reading with multilinguals. The key resources that emerge in the analyses encompass different forms of expression, hence multimodality is used as the overarching theoretical perspective in the study. Additionally, we discuss how good opportunities for promoting diverse reading practices become evident when kindergarten staff demonstrate curiosity, creativity, and a problem-solving approach to reading with multilinguals.

A nucleic acid binding protein map of germline regulation in Caenorhabditis elegans

Fertility requires the faithful proliferation of germ cells and their differentiation into gametes. Controlling these cellular states demands precise timing and expression of gene networks. Nucleic acid binding proteins (NBPs) play critical roles in gene expression networks that influence germ cell development. There has, however, been no functional analysis of the entire NBP repertoire in controlling in vivo germ cell development. Here, we analyzed germ cell states and germline architecture to systematically investigate the function of 364 germline-expressed NBPs in the Caenorhabditis elegans germ line. Using germline-specific knockdown, automated germ cell counting, and high-content analysis of germ cell nuclei and plasma membrane organization, we identify 156 NBPs with discrete autonomous germline functions. By identifying NBPs that control the germ cell cycle, proliferation, differentiation, germline structure and fertility, we have created an atlas for mechanistic dissection of germ cell behavior and gamete production.

Perimenopausal and Menopausal Mammary Glands In A 4-Vinylcyclohexene Diepoxide Mouse Model

As both perimenopausal and menopausal periods are recognized critical windows of susceptibility for breast carcinogenesis, development of a physiologically relevant model has been warranted. The traditional ovariectomy model causes instant removal of the entire hormonal repertoire produced by the ovary, which does not accurately approximate human natural menopause with gradual transition. Here, we characterized the mammary glands of 4-vinylcyclohexene diepoxide (VCD)-treated animals at different time points, revealing that the model can provide the mammary glands with both perimenopausal and menopausal states. The perimenopausal gland showed moderate regression in ductal structure with no responsiveness to external hormones, while the menopausal gland showed severe regression with hypersensitivity to hormones. Leveraging the findings on the VCD model, effects of a major endocrine disruptor (polybrominated diphenyl ethers, PBDEs) on the mammary gland were examined during and after menopausal transition, with the two exposure modes; low-dose, chronic (environmental) and high-dose, subacute (experimental). All conditions of PBDE exposure did not augment or compromise the macroscopic ductal reorganization resulting from menopausal transition and/or hormonal treatments. Single-cell RNA sequencing revealed that the experimental PBDE exposure during the post-menopausal period caused specific transcriptomic changes in the non-epithelial compartment such as Errfi1 upregulation in fibroblasts. The environmental PBDE exposure resulted in similar transcriptomic changes to a lesser extent. In summary, the VCD mouse model provides both perimenopausal and menopausal windows of susceptibility for the breast cancer research community. PBDEs, including all tested models, may affect the post-menopausal gland including impacts on the non-epithelial compartments.

Complete persistence of the primary somatosensory system in zebrafish

The somatosensory system detects peripheral stimuli that are translated into behaviors necessary for survival. Fishes and amphibians possess two somatosensory systems in the trunk: the primary somatosensory system, formed by the Rohon-Beard neurons, and the secondary somatosensory system, formed by the neural crest cell-derived neurons of the Dorsal Root Ganglia. Rohon-Beard neurons have been characterized as a transient population that mostly disappears during the first days of life and is functionally replaced by the Dorsal Root Ganglia. Here, I follow Rohon-Beard neurons in vivo and show that the entire repertoire remains present in zebrafish from 1-day post-fertilization until the juvenile stage, 15-days post-fertilization. These data indicate that zebrafish retain two complete somatosensory systems until at least a developmental stage when the animals display complex behavioral repertoires.

Learning from a community bilingual classroom: Toward a translanguaging literacies pedagogy with Chinese American bilinguals

ABSTRACT Situated in the Midwest region of the United States, this study draws on translanguaging literacies to critically examine the discussions and sense-making that was taking place in a Mandarin-English bilingual community classroom between a Chinese bilingual teacher and three Chinese American bilingual students while engaging in discussions of language, culture, and history with children’s literature. Our findings demonstrate that the teacher carefully applied translanguaging literacies as deliberate pedagogy to help bilingual students understand language in the world, normalize linguistic freedom and respect, and critically make sense of their complex identities and histories with and through their entire linguistic repertoires.

Stepwise Ultra-pH-Sensitive Micelles Overcome a pKa Barrier for Systemic Lymph Node Delivery.

While local nanoparticle delivery to lymph nodes is well studied, there are few design criteria for intravenous delivery to the entire lymph node repertoire. In this study, we investigated the effect of NP pH transition on lymph node targeting by employing a series of ultra-pH-sensitive (UPS) polymeric micelles. The UPS library responds to pH thresholds (pKa 6.9, 6.2, and 5.3) over a range of physiological pH. We observed a dependence of intravenous lymph node targeting on micelle pH transition. UPS6.9 (subscript indicates pKa) shows poor lymph node delivery, while UPS5.3 delivers efficiently to lymph node sets. We investigated targeting mechanisms of UPS5.3, observing an accumulation among lymph node lymphatics and a dependence on lymph node-resident macrophages. To overcome the pH-threshold barrier, which limits UPS6.9, we rationally designed a nanoparticle coassembly of UPS6.9 with UPS5.3, called HyUPS. The HyUPS micelle retains the constitutive pH transitions of each polymer, showing stepwise responses to discrete pH thresholds. We demonstrate that HyUPS improves UPS6.9 delivery to lymph nodes, extending this platform for disease detection of lymph node metastasis.

Step-by-step protocol for isolating the entire repertoire of human first trimester placental cells

Correct placental development and function are essential for adapting the mother to the ongoing pregnancy and the wellbeing of the growing fetus; however, underlying processes are still poorly understood. Only limited structural and cellular placental features are shared among species hence requiring reliable human in-vitro models. Recently established trophoblast stem cell and organoid models significantly improved placental research; however, the human placenta constitutes a multi-cellular organ with tightly orchestrated, cellular and molecular networks between trophoblasts (TBs) and villous core cells (VCCs) vital for correct placentation. The establishment of co-culture models is accordingly the logical consequence to investigate TB and VCC interactions, but first requires efficient purification of ideally donor-matched placental cell types. We herein present a meticulously-tailored protocol based on four sequential digestion steps (d-steps) with varying enzyme compositions and digestion mode and length, gently releasing cells layer-by-layer from human first trimester placentae (8 – 9th week of gestation). Using immunofluorescence and flow cytometry, we analyzed the tissue fragments and digestion solutions after every d-step and collected data on individual digestion progress as well as cell viability, counts, and specifications. D-step 1 revealed a significantly low viability and was mainly composed of syncytial fragments, extravillous trophoblasts EVTs, and maternal leukocytes. D-step 2 and 3, comprising high viability predominantly contained TBs (90 – 99 %) with a significant enrichment of EVTs in d-step 2 and an almost pure villous cytotrophoblast (vCTB) population in d-step 3. D-step 4 finally enabled isolating fetal VCCs consisting of endothelial cells, fibroblasts, and Hofbauer cells. Interestingly, maternal leukocytes were detected in d-step 1 and 2 but completely absent from d-step 3 and 4 revealing pure fetal cell populations. In sum, we present a detailed guideline for stepwise isolating selected placental cell types suitable for further studies and co-culture models investigating TB and VCC interactions involved in early placental development.

Principles of peptide selection by the transporter associated with antigen processing

Our ability to fight pathogens relies on major histocompatibility complex class I (MHC-I) molecules presenting diverse antigens on the surface of diseased cells. The transporter associated with antigen processing (TAP) transports nearly the entire repertoire of antigenic peptides into the endoplasmic reticulum for MHC-I loading. How TAP transports peptides specific for MHC-I is unclear. In this study, we used cryo-EM to determine a series of structures of human TAP, both in the absence and presence of peptides with various sequences and lengths. The structures revealed that peptides of eight or nine residues in length bind in a similarly extended conformation, despite having little sequence overlap. We also identified two peptide-anchoring pockets on either side of the transmembrane cavity, each engaging one end of a peptide with primarily main chain atoms. Occupation of both pockets results in a global conformational change in TAP, bringing the two halves of the transporter closer together to prime it for isomerization and ATP hydrolysis. Shorter peptides are able to bind to each pocket separately but are not long enough to bridge the cavity to bind to both simultaneously. Mutations that disrupt hydrogen bonds with the N and C termini of peptides almost abolish MHC-I surface expression. Our findings reveal that TAP functions as a molecular caliper that selects peptides according to length rather than sequence, providing antigen diversity for MHC-I presentation.

Macedonian ballet (1949 – 2024), decoding of diverse choreographic “letters”

This article attempts to determine the relevant processes related to ballet, positioned in a concrete geographic space–the Republic of Macedonia. The time frame starts with the year of the founding of the professional ballet ensemble within the Macedonian National Theatre (MNT) 1949 and ends with the year 2024. An additional reason for such a theoretical review is the celebration of the 75th anniversary of the Macedonian ballet. Due to the volume of material, the author decided to detect general styles, that is, general “chapters” or “letters” (as will be defined in the article), with their specific tendencies. From an analysis of the entire repertoire, performances can be classified into three general groups. The first is classical ballet with a fixed choreography (in Macedonia’s case, versions currently performed in Russia, that is, countries of the former Soviet Union). The second group is performances classified as contemporary regarding theme and music, but most importantly dance style. The third group is the works where there is a symbiosis between classical ballet and folk dance, which are referred to as national ballets. This group carries the most important and most distinctive national features. Each of the aforementioned groups is in close interaction with cultural politics, that is, current societal trends, which will be further elaborated.

A Multilevel Classification of Căluș Tunes (Argeș County)

The Ethnomusicological Study of Căluș Dances became part of the research plan of the Institute of Ethnography and Folklore “Constantin Brăiloiu”. The analysed corpus of the Călușul in Argeș consists of 200 tunes recorded by ethno-choreologist Anca Giurchescu, as direct observation or as re-enactment, and fully transcribed. In order to obtain a valid classification, we considered that the analysing terms should gather pieces with common features. Accordingly, we selected three coalescing parameters for defining the characteristics of this repertoire. This analysis led to a classification with 12 categories, infra-classes, which can be gradually grouped in sub-classes and, at a superior level, in classes. The special feature of our approach resides in the fact that these are interchangeable, which allows alternative multilevel classifications, in any necessary order. We consider that the analytical potential of the alternative multi-level classification is significant in highlighting the system of preferential relations created between hythmic, architectonic and melodic structures at the level of the entire repertoire. Keywords: rhythmic, architectonic, melodic level, multilevel classification.

Abstract 1869: The AI-powered KisoSeek™ platform identifies functional anti-TROP2 heavy-chain antibodies with potent anti-cancer activity

Abstract Functional heavy-chain antibodies (HCAbs) are promising therapeutic agents for targeted cancer therapy. Since they do not have a light chain, HCAbs have a small antigen-binding domain that can unlock new functionalities by reaching epitopes that are inaccessible to classical antibodies. HCAbs can be obtained by immunizing camelids, but this approach is expensive, time-consuming, and results in a limited antibody repertoire. Previously, we engineered the KisoMouse™- a transgenic mouse with multi-camelid species VHH/VH genes and the complete alpaca D and J gene segments integrated into the mouse IgH locus, along with a functional loss of the heavy chain CH1 domain to eliminate light chain pairing. KisoMouse™ are healthy and generate a robust serum HCAb response against a diverse range of immunogens. Trophoblast cell surface antigen-2 (TROP2) is a membrane protein overexpressed in numerous solid tumor types such as breast, colon, and lung cancers. TROP2 is associated with tumor aggressiveness and decreased survival and has emerged as an attractive therapeutic target. An anti-TROP2 antibody-drug conjugate has been approved for breast and bladder cancer, but challenges related to payload toxicity and resistance highlight the need for alternative therapeutics. We had previously identified an anti-TROP2 HCAb with high potency in in vivo preclinical models of human breast and colorectal cancer. Conventional antibody discovery approaches are resource-intensive and can fail to identify rare antibodies. To overcome such limitations, we developed the KisoSeek™ platform, a proprietary AI-powered toolkit that categorizes antibodies in an immune response based on their structural and biophysical features. With KisoSeek™, we analyzed the entire antibody repertoire generated from KisoMouse™ immunized with TROP2 and rapidly identified HCAbs with similar features as the high potency reference antibody described above. We selected three additional antibodies based on their in vitro TROP2 affinity, competitiveness for the reference antibody’s epitope, and yield in CHO cells. These candidates showed comparable potent efficacy in inducing regression in human breast and colorectal xenograft models, akin to the original reference antibody. In summary, the KisoSeek™ platform identified novel anti-TROP2 HCAbs out of the KisoMouse™ antibody repertoire that were similar to our original reference antibody. This demonstrates how KisoMouse™ and KisoSeek™ are two powerful complementary platforms for novel clinical antibody discovery. By categorizing the entire antibody repertoire and identifying antibodies with similar characteristics as known functional antibodies, KisoSeek™ has the potential to leverage existing discovery efforts to uncover many more rare yet potent therapeutic antibodies - the proverbial needles in a haystack. Citation Format: Sophie E. Cousineau, Amit Subedi, Richard Wargachuk, Juliana The, Xiaowei Wang, Wenyang Hou, Amogh Nair, Wansu Qiu, Alex Zhou, Tiffany Cheng, Morteza Babaie, Benyamin Gojogh, Marinieve Montero, Hiba Zahreddine, Elijus Undzys, Lucy Lai, Gordon Ngan, Luis Da Cruz, David Young. The AI-powered KisoSeek™ platform identifies functional anti-TROP2 heavy-chain antibodies with potent anti-cancer activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1869.

A Detailed Protocol for Constructing a Human Single-Chain Variable Fragment (scFv) Library and Downstream Screening via Phage Display.

The development of monoclonal antibodies (mAbs) represents a significant milestone in both basic research and clinical applications due to their target specificity and versatility in therapeutic and diagnostic applications. The innovative strategy of mAb screening, utilizing phage display, facilitates the in vitro screening of antibodies with high affinity to target antigens. The single-chain variable fragment (scFv) is a subset of mAb derivatives, known for its high binding affinity and smaller size-just one-third of that of human IgG. This report outlines a detailed and comprehensive procedure for constructing a scFv phagemid library derived from human patients, followed by screening via phage display affinity selection. The protocol utilizes 348 primer combinations spanning the entire human antibody repertoire to minimize sequence bias and maintain library diversity during polymerase chain reaction (PCR) for scFv generation, resulting in a library size greater than 1 × 108. Furthermore, we describe a high-throughput phage display screening protocol using enzyme-linked immunosorbent assay (ELISA) to evaluate more than 1200 scFv candidates. The generation of a highly diverse scFv library, coupled with the implementation of a phage display screening methodology, is expected to provide a valuable resource for researchers in pursuit of scFvs with high affinity for target antigens, thus advancing both research and clinical endeavors.

Highly heterogenous humoral immune response in Lyme disease patients revealed by broad machine learning-assisted antibody binding profiling with random peptide arrays.

Lyme disease (LD), a rapidly growing public health problem in the US, represents a formidable challenge due to the lack of detailed understanding about how the human immune system responds to its pathogen, the Borrelia burgdorferi bacterium. Despite significant advances in gaining deeper insight into mechanisms the pathogen uses to evade immune response, substantial gaps remain. As a result, molecular tools for the disease diagnosis are lacking with the currently available tests showing poor performance. High interpersonal variability in immune response combined with the ability of the pathogen to use a number of immune evasive tactics have been implicated as underlying factors for the limited test performance. This study was designed to perform a broad profiling of the entire repertoire of circulating antibodies in human sera at the single-individual level using planar arrays of short linear peptides with random sequences. The peptides sample sparsely, but uniformly the entire combinatorial sequence space of the same length peptides for profiling the humoral immune response to a B.burg. infection and compare them with other diseases with etiology similar to LD and healthy controls. The study revealed substantial variability in antibody binding profiles between individual LD patients even to the same antigen (VlsE protein) and strong similarity between individuals diagnosed with Lyme disease and healthy controls from the areas endemic to LD suggesting a high prevalence of seropositivity in endemic healthy control. This work demonstrates the utility of the approach as a valuable analytical tool for agnostic profiling of humoral immune response to a pathogen.

'Multilingualising' Language Education: A Teacher Training Programme for English as a 'Bridge Language' in Early Childhood Education

This article outlines a teacher training programme called: "English in the Kindergarten: Towards Multilingual Education", which was designed and implemented as a response to the introduction of English in Greek state preschools from 2021 onward. The programme aims to develop teachers' knowledge, skills, and attitudes for the introduction of the English language as a cross-linguistic and cross-cultural bridge and ultimately to promote multilingualism and inclusion in the class. It is theoretically grounded on a critical sociolinguistic approach toward languages in education, which valourises the children's entire linguistic repertoire and challenges 'parallel monolingualisms' that typify some initiatives in the field of early (foreign) language education. Classes are reimagined as spaces where learners and teachers engage with age-appropriate experiential and plurilingual practices, art-based learning, drama techniques, and puppetry. At the same time, pluralistic approaches and translanguaging are proposed to be used to leverage children's linguistic and cultural capitals as they engage with English in early language education, thus enhancing multilingual and intercultural awareness. After discussing the theoretical tenets of the program's design, an overview of its structure and sample activities is provided as well as extracts from participant teachers' output and data from its evaluation. The paper concludes with the implications of the programme and the perspective it advances.

Current advancements in B-cell receptor sequencing fast-track the development of synthetic antibodies.

Synthetic antibodies (Abs) are a class of engineered proteins designed to mimic the functions of natural Abs. These are produced entirely in vitro, eliminating the need for an immune response. As such, synthetic Abs have transformed the traditional methods of raising Abs. Likewise, deep sequencing technologies have revolutionized genomics and molecular biology. These enable the rapid and cost-effective sequencing of DNA and RNA molecules. They have allowed for accurate and inexpensive analysis of entire genomes and transcriptomes. Notably, via deep sequencing it is now possible to sequence a person's entire B-cell receptor immune repertoire, termed BCR sequencing. This procedure allows for big data explorations of natural Abs associated with an immune response. Importantly, the identified sequences have the ability to improve the design and engineering of synthetic Abs by offering an initial sequence framework for downstream optimizations. Additionally, machine learning algorithms can be introduced to leverage the vast amount of BCR sequencing datasets to rapidly identify patterns hidden in big data to effectively make in silico predictions of antigen selective synthetic Abs. Thus, the convergence of BCR sequencing, machine learning, and synthetic Ab development has effectively promoted a new era in Ab therapeutics. The combination of these technologies is driving rapid advances in precision medicine, diagnostics, and personalized treatments.

Recording Cilia Activity in Ctenophores.

Pelagic ctenophores swim in the water with the help of eight rows of long fused cilia. Their entire behavioral repertoire is dependent to a large degree on coordinated cilia activity. Therefore, recording cilia beating is paramount to understanding and registering the behavioral responses and investigating its neural and hormonal control. Here, we present a simple protocol to monitor and quantify cilia activity in semi-intact ctenophore preparations (using Pleurobrachia and Bolinopsis as models), which includes a standard electrophysiological setup for intracellular recording.

Current status of molecular diagnostics for lung cancer.

The management of lung cancer (LC) requires the analysis of a diverse spectrum of molecular targets, including kinase activating mutations in EGFR, ERBB2 (HER2), BRAF and MET oncogenes, KRAS G12C substitutions, and ALK, ROS1, RET and NTRK1-3 gene fusions. Administration of immune checkpoint inhibitors (ICIs) is based on the immunohistochemical (IHC) analysis of PD-L1 expression and determination of tumor mutation burden (TMB). Clinical characteristics of the patients, particularly age, gender and smoking history, significantly influence the probability of finding the above targets: for example, LC in young patients is characterized by high frequency of kinase gene rearrangements, while heavy smokers often have KRAS G12C mutations and/or high TMB. Proper selection of first-line therapy influences overall treatment outcomes, therefore, the majority of these tests need to be completed within no more than 10 working days. Activating events in MAPK signaling pathway are mutually exclusive, hence, fast single-gene testing remains an option for some laboratories. RNA next-generation sequencing (NGS) is capable of detecting the entire repertoire of druggable gene alterations, therefore it is gradually becoming a dominating technology in LC molecular diagnosis.

Classroom interaction in an online context: A translanguaging informed conversation analysis perspective

This study aims to investigate the mode-divergent practices of pre-service teachers in an online context. Firstly, 16 h of classroom interaction is analyzed via Conversation Analysis utilizing the Classroom Interactional Competence framework. Then, the translanguaging pedagogy perspective complements this analysis by focusing on linguistic, social, and psychological aspects. The conversation-analytical findings demonstrate the failures in constructive alignment, and an inordinate amount of wasted time with no satisfying results has been observed. It is shown that translanguaging pedagogy may support the creative, critical, and strategic utilization of bilingual students' entire repertoires in classroom practices. Overall, the analysis demonstrates how translanguaging pedagogies can inform mode-divergent practices in classrooms by which teachers’ interactional competence may be improved.