Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancing the anti-tumor efficacy of Bispecific T cell engagers via cell surface glycocalyx editing

Bispecific T-cell engager (BiTE)-based cancer therapies that activate the cytotoxic T cells of a patient’s own immune system have gained momentum with the recent FDA approval of Blinatumomab for treating B cell malignancies. However, this approach has had limited success in targeting solid tumors. Here, we report the development of BiTE-sialidase fusion proteins that enhance tumor cell susceptibility to BiTE-mediated cytolysis by T cells via targeted desialylation at the BiTE-induced T cell-tumor cell interface. Targeted desialylation results in better immunological synapse formation, T-cell activation and effector function. As a result, BiTE-sialidase fusion proteins show remarkably increased efficacy in inducing T-cell-dependent tumor cell cytolysis in response to target antigens compared to the parent BiTE molecules alone. This enhanced function is seen both in vitro and in in vivo xenograft and syngeneic solid tumor mouse models. Our findings highlight BiTE-sialidase fusion proteins as promising candidates for the development of next-generation bispecific T-cell engaging molecules for cancer immunotherapy.
Predictions of immunogenicity reveal potent SARS-CoV-2 CD8+ T-cell epitopes

The recognition of pathogen or cancer-specific epitopes by CD8+ T cells is crucial for the clearance of infections and the response to cancer immunotherapy. This process requires epitopes to be presented on class I Human Leukocyte Antigen (HLA-I) molecules and recognized by the T-Cell Receptor (TCR). Machine learning models capturing these two aspects of immune recognition are key to improve epitope predictions. Here we assembled a high-quality dataset of naturally presented HLA-I ligands and experimentally verified neo-epitopes. We then integrated these data with new algorithmic developments to improve predictions of both antigen presentation and TCR recognition. Applying our tool to SARS-CoV-2 proteins enabled us to uncover several epitopes. TCR sequencing identified a monoclonal response in effector/memory CD8+ T cells against one of these epitopes and cross-reactivity with the homologous SARS-CoV-1 peptide.
Rapid, in-patient adaptations of Legionella pneumophila to the human host

Legionella pneumophila are host-adapted bacteria that infect and reproduce primarily in amoeboid protists. Using similar infection mechanisms, they infect human macrophages, and cause Legionnaires’ disease, an atypical pneumonia, and the milder Pontiac fever. We hypothesized that, despite these similarities, the hosts are different enough so that there exist high-selective value mutations that would dramatically increase the fitness of Legionella inside the human host. By comparing a large number of isolates from independent infections, we identified two genes, mutated in three unrelated patients, despite the short duration of the incubation period (2-14 days). One is a gene coding for an outer membrane protein (OMP) belonging to the OmpP1/FadL family. The clinical strain, carrying the mutated OMP homolog, grows faster in macrophages than the wild type strain, and thus appears to be better adapted to the human host. The other is a gene coding for a protein involved in cyclic-di-GMP regulation, which in turn modulates flagellar activity. As human-to-human transmission is very rare, fixation of these mutations into the population and spread into the environment is unlikely. Therefore, convergent evolution – here mutations in the same genes observed in independent human infections – could point to adaptations to the accidental human host. These results suggest that despite its ability to infect, replicate, and disperse from amoebae, L. pneumophila is not well adapted to the human host. Impact statement Legionella pneumophila is primarily infecting amoeboid protists, but occasionally infects human lung macrophages, causing Legionnaires’ disease, an atypical pneumonia. By comparing 171 isolates from patients to their probable environmental source, we identified 119 mutations that presumably occurred in-patient. Among these, several mutations occurred in the gene. In particular, two genes were mutated thrice, significantly more often than expected by chance alone, and are likely to represent adaptations to the human host. We experimentally show that, for one mutation at least, the mutated strain grows faster in human macrophages than in amoebae. By specifically investigating in-patient mutations, we were able to identify two genes that might be involved in human host-specific adaptations of L. pneumophila. This result suggests that L. pneumophila is not particularly well adapted to the human host, as mutations get fixed in-patient, during the short course of an infection (2-14 days), indicating a very high selective value. Data Summary The sequencing data generated in this study are available in the NCBI database under the BioProject accession number: PRJEB52976.
Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines

When should vaccines to evolving pathogens such as SARS-CoV-2 be updated? Our computational models address this focusing on updating SARS-CoV-2 vaccines to the currently circulating Omicron variant. Current studies typically compare the antibody titers to the new variant following a single dose of the original-vaccine versus the updated-vaccine in previously immunized individuals. These studies find that the updated-vaccine does not induce higher titers to the vaccine-variant compared with the original-vaccine, suggesting that updating may not be needed. Our models recapitulate this observation but suggest that vaccination with the updated-vaccine generates qualitatively different humoral immunity, a small fraction of which is specific for unique epitopes to the new variant. Our simulations suggest that these new variant-specific responses could dominate following subsequent vaccination or infection with either the currently circulating or future variants. We suggest a two-dose strategy for determining if the vaccine needs updating and for vaccinating high-risk individuals.
Tle4 controls both developmental acquisition and postnatal maintenance of corticothalamic projection neuron identity

Identities, circuitry, and function of distinct neuron subtypes are specified during embryonic development, then maintained during postnatal maturation and potential plasticity. Mechanisms that control early acquisition of neuron subtype identities, encompassing circuitry and function, in the cerebral cortex have become increasingly understood. However, mechanisms controlling maintenance of identity, and accompanying regulation of plasticity, are largely unexplored and unknown. Here, we identify two novel functions of the co-repressor Tle4 in both acquisition and maintenance of neuron subtype identity of corticothalamic projection neurons. Embryonically, Tle4 promotes acquisition of corticothalamic molecular and cellular identity, and blocks emergence of core characteristics of subcerebral / corticospinal projection neuron identity, including morphology, gene expression, axonal connectivity, and circuitry. Postnatally, Tle4 is required to maintain corticothalamic molecular and projection identity during circuit maturation, avoiding potentially disruptive plasticity, but also limiting potentially beneficial plasticity. We identify an epigenetic mechanism by which TLE4 controls the activation state of loci regulating the level of Fezf2 expression by corticothalamic neurons during embryonic and postnatal development. This mechanism contributes importantly to distinction of cortical output (corticofugal) subtypes, and ensures appropriate maturation and maintenance of CThPN. Highlights Tle4 promotes CThPN identity and blocks SCPN identity in early-born cortical neurons Tle4 is necessary to maintain CThPN identity during circuit maturation TLE4-FEZF2 complex epigenetically regulates Fezf2 expression in developing CThPN TLE4-FEZF2 regulates corticofugal subtypes distinction and maturation of CThPN
Incilius alvarius cell-based synthesis of 5-MeO-DMT

There is growing interest in the therapeutic potential of 5-MeO-DMT (5-methoxy-N,N-dimethyltryptamine) for psychiatric disorders. While 5-MeO-DMT can be chemically synthesized, the parotoid gland secretions of Incilius alvarius (also known as the Colorado River or Sonoran Desert toad) contain 5-MeO-DMT and other molecules including bufotenine, bufagenins, bufotoxins, and indole alkylamines that may have individual clinical utility or act as entourage molecules to enhance the activity of 5-MeO-DMT. Incilius alvarius is currently under severe ecological pressure due to demand for natural 5-MeO-DMT and habitat loss. We established a cell line from tissue obtained by wedge biopsy from the parotoid gland of Incilius alvarius and confirmed the cell-based synthesis of 5-MeO-DMT by LC-MS/MS. Cell-based biosynthesis of Incilius alvarius parotoid gland secretions is a potentially cruelty-free and sustainable source of naturally derived 5-MeO-DMT for research and drug development. Graphical Abstract
Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover

Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide, once validated, a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover. Key message High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding.
Distinct Effects of the Apolipoprotein E ε4 Genotype on Associations Between Delayed Recall Performance and Resting-State Electroencephalography Theta Power in Elderly People Without Dementia

Background Abnormal electroencephalography (EEG) activity has been demonstrated in mild cognitive impairment (MCI), and theta rhythm might be inversely related to memory. The apolipoprotein E (ApoE) epsilon 4 (ε4) allele, as a genetic vulnerability factor for pathologic and normal age-related cognitive decline, may influence different patterns of cognitive dysfunction. Therefore, the present study primarily aimed to verify the role of resting theta rhythm in delayed recall deficits, and further explore the effects of the ApoE genotype on the associations between the resting theta power and delayed recall performance in the elderly individuals without dementia. Methods A total of 47 individuals without dementia, including 23 MCI and 24 healthy subjects (HCs), participated in the study. All subjects were administered the Hopkins Verbal Learning Test–Revised (HVLT-R) to measure delayed recall performance. Power spectra based on resting-state EEG data were used to examine brain oscillations. Linear regression was used to examine the relationships between EEG power and delayed recall performance in each subgroup. Results The increased theta power in the bilateral central and temporal areas (Ps = 0.02–0.044, uncorrected) was found in the patients with MCI, and were negatively correlated with delayed recall performance (rs = −0.358 to −0.306, Ps = 0.014–0.036, FDR corrected) in the elderly individuals without dementia. The worse delayed recall performance was associated with higher theta power in the left central and temporal areas, especially in ApoE ε4 non-carriers and not in carriers (rs = −0.404 to −0.369, Ps = 0.02–0.035, uncorrected). Conclusion Our study suggests that theta disturbances might contribute to delayed recall memory decline. The ApoE genotype may have distinct effects on EEG-based neural correlates of episodic memory performance.
Peritoneal Protein Loss, Inflammation, and Nutrition: Refuting Myths

Peritoneal protein loss (PPL) has been correlated with mortality, malnutrition and inflammation. More recently overhydration was brought to the equation. This study aims to review classic and recent factors associated with PPL. Prevalent and incident peritoneal dialysis (PD) patients were included. Dialysate and serum IL-6 was obtained during PET. Hydration and nutritional status were assessed by bio-impedance. Linear regression and Cox regression were performed. The 78 included patients presented median values of PPL 4.8 g/24 h, serum IL-6: 5.1 pg/mL, and IL-6 appearance rate 153.5 pg/min. Mean extracellular water excess (EWexc) was 0.88 ± 0.94 L, and lean body mass index (LBMI) 17.3 ± 2.4 kg/m2. After mean follow-up of 33.9 ± 29.3 months, 12 patients died. Linear univariable analysis showed positive associations between PPL and small solute transport, body composition (LBMI and EWexc), comorbidities and performing CAPD (vs. cycler). PPL correlated positively with dialysate appearance rate of IL-6, but not with serum IL-6. Linear multivariable analysis confirmed positive association between PPL and EWexc (p = 0.012; 95%CI: 4.162–31.854), LBMI (p = 0.008; 95%CI: 1.720–11.219) and performing CAPD (p = 0.023; 95%CI: 4.375–54.190). In survival analysis, no relationship was found between mortality and PPL. Multivariable Cox regression showed Charlson Comorbidity Index (HR: 1.896, 95%CI: 1.235–2.913), overhydration (HR: 10.034, 95%CI: 1.426–70.587) and lower PPL (HR: 0.576, 95%CI: 0.339–0.978) were predictors for mortality. Overhydration, was a strong predictor of PPL, overpowering variables previously reported as determinants of PPL, namely clinical correlates of endothelial dysfunction or local inflammation. PPL were not associated with malnutrition or higher mortality, emphasizing the importance of volume overload control in PD patients.
Regulatory Role and Potential Importance of GDF-8 in Ovarian Reproductive Activity

Growth differentiation factor-8 (GDF-8) is a member of the transforming growth factor-beta superfamily. Studies in vitro and in vivo have shown GDF-8 to be involved in the physiology and pathology of ovarian reproductive functions. In vitro experiments using a granulosa-cell model have demonstrated steroidogenesis, gonadotrophin responsiveness, glucose metabolism, cell proliferation as well as expression of lysyl oxidase and pentraxin 3 to be regulated by GDF-8 via the mothers against decapentaplegic homolog signaling pathway. Clinical data have shown that GDF-8 is expressed widely in the human ovary and has high expression in serum of obese women with polycystic ovary syndrome. GDF-8 expression in serum changes dynamically in patients undergoing controlled ovarian hyperstimulation. GDF-8 expression in serum and follicular fluid is correlated with the ovarian response and pregnancy outcome during in vitro fertilization. Blocking the GDF-8 signaling pathway is a potential therapeutic for ovarian hyperstimulation syndrome and ovulation disorders in polycystic ovary syndrome. GDF-8 has a regulatory role and potential importance in ovarian reproductive activity and may be involved in folliculogenesis, ovulation, and early embryo implantation.
Access Barriers to Dental Treatment and Prevention for Turkish Migrants in Germany – A Qualitative Survey

Introduction The worldwide migration movement is growing and thereby challenging the health care systems of immigration countries like Germany to make health care equally accessible for all people. Due to their low oral health status and low uptake rates of dental treatment and prevention, migrants were detected as a vulnerable group. Data regarding dental care access barriers of this group is limited. Therefore, the following study established a deeper understanding of unknown access barriers. Methods Nine expert interviews and one focus group interview were conducted semi-structured via interview guideline in the period of August until October 2018. The experts were persons with strong vocational interactions and experiences with the sector oral health care and migration. The focus group participants had a Turkish migration background. Results The expert and focus group interviews revealed a variety of barriers that exist toward dental treatment and prevention for migrants. Language, perceived significance of oral health, oral health knowledge, health socialization and patient-dentist interaction were detected to be the main barriers with underlying subthemes and interactions. Furthermore, a predominantly not precaution-oriented dental service utilization of migrants was underlined by the interviewees. Additionally, ways to reach a higher cultural sensitivity in oral health care were stated. Conclusion With respect for research, there is a need for the integration of migrant-specific items when collecting health data from people. With respect for policy, there is a need for more structural and individual attention for promoting equal access to oral health care and prevention measures for people with a migrant background.
Understanding Behavior in Phelan-McDermid Syndrome

Background Phelan-McDermid syndrome (PMS) or 22q13.3 deletion syndrome is a rare genetic disorder characterized by developmental delay, hypotonia and severely delayed speech. Behavioral difficulties are often reported in PMS, although knowledge of behavioral profiles and the interpretation of reported behavior remains limited. Understanding the meaning of behavior requires considering the context as well as other domains of functioning, for example the individual's level of cognitive, social and emotional development. Combining structured direct in-person neurodevelopmental assessments with contextual assessments to enable meaningful interpretations of reported behavior on functional dimensions across multiple units of analysis, as proposed by the RDoc framework, is essential. Methods In this article we present a structured multidisciplinary method of assessment through direct in-person neurodevelopmental assessments and assessment of contextual factors. Our study sample includes data of 33 children with an average age of 6.2 years (range 1.1 to 15.7) with PMS, obtained through individual in-person assessments in combination with parent informed questionnaires. We assessed developmental age using the Bayley-III, adaptive behavior was assessed with the Vineland screener, social-emotional development with the ESSEON-R and behavior by using the CBCL. Results Our results show a great deal of variability in phenotypic presentation with regard to behavior, symptom expression and symptom severity in individuals with PMS. The data on behavior is interpreted in the context of the individual's level of cognitive, adaptive development and the (genetic) context. Behavioral data showed high levels of withdrawn behavior and attention problems. More than half of the children showed borderline or clinical symptoms related to Autism Spectrum Disorder (ASD). Conclusions The interpretation of the meaning of certain behavior in PMS is often based on questionnaires and descriptions without taking the specific context of development into account. Combining questionnaires with direct in-person assessments measuring different domains of functioning should be considered a more accurate method to interpret the meaning of findings in order to understand behavior in rare genetic disorders associated with developmental delay such as PMS. Direct in-person assessment provides valuable and specific information relevant to understanding individual behavior and inform treatment as well as increase knowledge of the neurodevelopmental phenotype in individuals with PMS. More specific application of the proposed frameworks on behavior in PMS is desirable in making useful interpretations.
Association Mapping of Drought Tolerance Indices in Ethiopian Durum Wheat (Triticum turgidum ssp. durum)

Ethiopia is a major producer of durum wheat in sub-Saharan Africa. However, its production is prone to drought stress as it is fully dependent on rain, which is erratic and unpredictable. This study aimed to detect marker-trait associations (MTAs) and quantitative trait loci (QTLs) related to indices. Six drought tolerance indices, i.e., drought susceptibility index (DSI), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), and yield stability index (YSI) were calculated from least-square means (lsmeans) of grain yield (GY) and traits significantly (p < 0.001) correlated with grain yield (GY) under field drought stress (FDS) and field non-stress (FNS) conditions. GY, days to grain filling (DGF), soil plant analysis development (SPAD) chlorophyll meter, seeds per spike (SPS), harvest index (HI), and thousand kernel weight (TKW) were used to calculate DSI, GMP, RDI, STI, TOL, and YSI drought indices. Accessions, DW084, DW082, DZ004, C037, and DW092 were selected as the top five drought-tolerant based on DSI, RDI, TOL, and YSI combined ranking. Similarly, C010, DW033, DW080, DW124-2, and C011 were selected as stable accessions based on GMP and STI combined ranking. A total of 184 MTAs were detected linked with drought indices at –log10p ≥ 4.0,79 of which were significant at a false discovery rate (FDR) of 5%. Based on the linkage disequilibrium (LD, r2 ≥ 0.2), six of the MTAs with a positive effect on GY-GMP were detected on chromosomes 2B, 3B, 4A, 5B, and 6B, explaining 14.72, 10.07, 26.61, 21.16, 21.91, and 22.21% of the phenotypic variance, respectively. The 184 MTAs were clustered into 102 QTLs. Chromosomes 1A, 2B, and 7A are QTL hotspots with 11 QTLs each. These chromosomes play a key role in drought tolerance and respective QTL may be exploited by marker-assisted selection for improving drought stress tolerance in wheat.