bluuebunny/crossref_metadata_2025 huggingface dataset:
Learning and consolidating the contextualized contour representations of tones from F0 sequences and durational variations via transformers
Authors: Liu Yi-Fen , Lu Xiang-Li
Published: November 2024

Many speech characteristics, including conventional acoustic features such as mel frequency cepstrum coefficients and mel-spectrograms, as well as pre-trained contextualized acoustic representations such as wav2vec2.0, are used in a deep neural network or successfully fine-tuned with a connectionist temporal classification for Mandarin tone classification. In this study, the authors propose a transformer-based tone classification architecture, TNet-Full, which uses estimated fundamental frequency (F0) values and aligned boundary information on syllables and words. Key components of the model framework are the contour encoder and rhythm encoder, as well as the cross-attention between contours and rhythms established in the interaction encoder. Using contextual tonal contours as a reference, as well as rhythmic information derived from duration variations to consolidate more on contour representations for tone recognition, TNet-Full achieves absolute performance improvements of 24.4% for read speech (from 71.4% to 95.8%) and 6.3% for conversational speech (from 52.1% to 58.4%) when compared to a naive, simple baseline transformer, TNet-base. The relative improvements are 34.2% and 12.1%. As humans perceive tones, contour abstractions of tones can only be derived from F0 sequences, and tone recognition would be improved if syllable temporal organization was stable and predictable instead of fluctuating as seen in conversations.
The Effect of Corrective Exercises on Ground Reaction Forces in Male Students With Upper Crossed Syndrome During Throwing
Authors: Sakinepoor Ainollah , Degens Hans , Ahmadi Poria , Nazari Sagher , Mazidi Maryam
Published: November 2024

Purpose: Poor posture has a negative impact on physical capability and is associated with changes in biomechanics and motor control. The purpose of this study was to assess the effect of corrective exercises on ground reaction forces (GRFs) in male student handball players with upper crossed syndrome (UCS) during throwing. Methods: Thirty male handball students with UCS participated in this single-blind randomized controlled trial (IRCT20200622047888N2; IR.HUMS.REC.1402.135). Fifteen received an 8-week corrective exercise intervention (exercise-intervention group [EG]), consisting of exercise targeting muscles involved in the UCS, and 15 served as the control group (CG). During handball throwing, GRF was measured by force plate. The forward head and rounded shoulder angles were measured with a photogrammetric method. All measurements were repeated 8 weeks later. Results: Significant interactions for virtually all parameters indicated that changes over 8 weeks differed between the CG and EG. A reduction in GRFs and a delayed occurrence of peak GRFs were observed in the EG, but not in the CG (P < .05). This was accompanied by a significant reduction in forward head (P < .03; effect size: 0.87; 95% confidence interval, −2.34 to 0.13), rounded shoulder (P < .05; effect size: 0.68; 95% confidence interval, 0.32 to 1.22) and thoracic kyphosis (P < .02; effect size: 0.64; 95% confidence interval, 0.54 to 1.25) angles in the EG (P < .05) with no significant change over 8 weeks in the CG. Conclusion: Corrective exercises targeting muscles directly involved in UCS induces functional and postural improvements in male student handball players with UCS.
A Case Study and Guide for Sport Data Analytics: Using Python and Yahoo! Finance Data to Run Practical Analyses in the Sport Management Classroom
Authors: Damon Zack J. , Ellis Michael E.
Published: November 2024

Sport analytics remains a growing area in the sport industry. As such, the demand for skills and knowledge in this area has grown. This demand includes off-field data, such as marketing trends, as well as financial data related to sport organizations. There has been a trickle-down effect in sport management (and other) education programs to teach about analytics to better prepare students for these positions. The current case study will help instructors teach students analytics skills related to data exploration and analysis through Python, a common analytics and coding program. The case study presents an overview of the importance of sport analytics in the industry. We then present the code to be used in teaching a class related to scraping financial data from Yahoo!Finance and provide sample analyses with related code for assignments.
Integration of horizontally acquired light-harvesting genes into an ancestral regulatory network in the cyanobacterium
Acaryochloris marina
MBIC11017
Authors: Ulrich Nikea J. , Miller Scott R.
Published: November 2024

The acquisition of new capabilities by horizontal gene transfer (HGT) shapes the distribution of traits during microbial diversification. In the Chlorophyll (Chl)
d
-producing cyanobacterium
Acaryochloris marina
, the genes involved in the production and disassembly of the light-harvesting phycobiliprotein phycocyanin (PC) were lost in the
A. marina
common ancestor but then subsequently regained via HGT in
A. marina
strain MBIC11017. However, it remains unknown how the HGT-acquired PC genes in MBIC11017 have been reintegrated into its existing regulatory network after tens of millions of years since their loss. Here, we investigated potential mechanisms of regulatory assimilation of PC genes by comparing the transcriptomes of
A. marina
strain MBIC11017 and a PC-lacking close relative under both low irradiance far-red light and high irradiance white light. We found that PC assembly and degradation processes have been re-assimilated into a conserved ancestral response to high light. Further, we identified putative regulatory elements that were likely co-transferred with PC genes and could be recognized by
A. marina
’s pre-existing light response machinery. This study offers insights into how HGT-acquired genes can be reintegrated into an existing transcriptional regulatory network that has evolved in their absence.

IMPORTANCE

Horizontal gene transfer, the asymmetric movement of genetic information between donor and recipient organisms, is an important mechanism for acquiring new traits. In order for newly acquired gene content to be retained, it must be integrated into the genetic repertoire and regulatory networks of the recipient cell. In a strain of the Chlorophyll
d
-producing cyanobacterium
Acaryochloris marina
, the recent reacquisition of the genes required to produce the light-harvesting pigment phycocyanin offers a rare opportunity to understand the mechanisms underlying the regulatory assimilation of an acquired complex trait in bacteria. The significance in our research is in characterizing how an ancestrally lost, complex trait can be reintegrated into a conserved regulatory network, even after millions of years.
RNAseq and targeted metabolomics implicate RIC8 in regulation of energy homeostasis, amino acid compartmentation, and asexual development in
Neurospora crassa
Authors: Quinn Monique , Carrillo Alexander J. , Halilovic Lida , Borkovich Katherine A.
Published: November 2024

Heterotrimeric G protein signaling pathways control growth and development in eukaryotes. In the multicellular fungus
Neurospora crassa
, the guanine nucleotide exchange factor RIC8 regulates heterotrimeric Gα subunits. In this study, we used RNAseq and liquid chromatography-mass spectrometry (LC-MS) to profile the transcriptomes and metabolomes of
N. crassa
wild type, the Gα subunit mutants Δ
gna-1
and Δ
gna-3
, and Δ
ric8
strains. These strains exhibit defects in growth and asexual development (conidiation), with wild-type and Δ
gna-1
mutants producing hyphae in submerged cultures, while Δ
gna-3
and Δ
ric8
mutants develop conidiophores, particularly in the Δ
ric8
mutant. RNAseq analysis showed that the Δ
gna-1
mutant possesses 159 mis-regulated genes, while Δ
gna-3
and Δ
ric8
strains have more than 1,000 each. Many of the mis-regulated genes are involved in energy homeostasis, conidiation, or metabolism. LC-MS revealed changes in levels of primary metabolites in the mutants, with several arginine metabolic intermediates impacted in Δ
ric8
strains. The differences in metabolite levels could not be fully explained by the expression or activity of pathway enzymes. However, transcript levels for two predicted vacuolar arginine transporters were affected in Δ
ric8
mutants. Analysis of arginine and ornithine levels in transporter mutants yielded support for altered compartmentation of arginine and ornithine between the cytosol and vacuole in Δ
ric8
strains. Furthermore, we validated previous reports that arginine and ornithine levels are low in wild-type conidia. Our results suggest that RIC8 regulates asexual sporulation in
N. crassa
at least in part through altered expression of vacuolar transporter genes and the resultant mis-compartmentation of arginine and ornithine.

IMPORTANCE

Resistance to inhibitors of cholinesterase-8 (RIC8) is an important regulator of heterotrimeric Gα proteins in eukaryotes. In the filamentous fungus
Neurospora crassa
, mutants lacking ric8 undergo inappropriate asexual development (macroconidiation) during submerged growth. Our work identifies a role for RIC8 in regulating expression of transporter genes that retain arginine and ornithine in the vacuole (equivalent of the animal lysosome) and relates this function to the developmental defect. Arginine is a critical cellular metabolite, both as an amino acid for protein synthesis and as a precursor for an array of compounds, including proline, ornithine, citrulline, polyamines, creatine phosphate, and nitric oxide. These results have broad relevance to human physiology and disease, as arginine modulates immune, vascular, hormonal, and other functions in humans.
Similarities and distinctions in the activation of the
Candida glabrata
Pdr1 regulatory pathway by azole and non-azole drugs
Authors: Conway Thomas P. , Vu Bao Gia , Beattie Sarah R. , Krysan Damian J. , Moye-Rowley W. Scott
Published: November 2024

Incidences of fluconazole (FLC) resistance among
Candida glabrata
clinical isolates are a growing issue in clinics. The pleiotropic drug response network in
C. glabrata
confers azole resistance and is defined primarily by the Zn
2
Cys
6
zinc cluster-containing transcription factor Pdr1 and target genes such as
CDR1
, which encodes an ATP-binding cassette transporter protein thought to act as an FLC efflux pump. Mutations in the
PDR1
gene that render the transcription factor hyperactive are the most common cause of fluconazole resistance among clinical isolates. The phenothiazine class drug fluphenazine and a molecular derivative, CWHM-974, which both exhibit antifungal properties, have been shown to induce the expression of Cdr1 in
Candida
spp. We have used a firefly luciferase reporter gene driven by the
CDR1
promoter to demonstrate two distinct patterns of
CDR1
promoter activation kinetics: gradual promoter activation kinetics that occur in response to ergosterol limitations imposed by exposure to azole and polyene class antifungals and a robust and rapid
CDR1
induction occurring in response to the stress imposed by fluphenazines. We can attribute these different patterns of
CDR1
induction as proceeding through the promoter region of this gene since this is the only segment of the gene included in the luciferase reporter construct. Genetic analysis indicates that the signaling pathways responsible for phenothiazine and azole induction of
CDR1
overlap but are not identical. The short time course of phenothiazine induction suggests that these compounds may act more directly on the Pdr1 protein to stimulate its activity.

IMPORTANCE

Candida glabrata
has emerged as the second-leading cause of candidiasis due, in part, to its ability to acquire high-level resistance to azole drugs, a major class of antifungal that acts to block the biosynthesis of the fungal sterol ergosterol. The presence of azole drugs causes the induction of a variety of genes involved in controlling susceptibility to this drug class, including drug transporters and ergosterol biosynthetic genes such as ERG11. We found that the presence of azole drugs leads to an induction of genes encoding drug transporters and ERG11, while exposure of
C. glabrata
cells to antifungals of the phenothiazine class of drugs caused a much faster and larger induction of drug transporters but not ERG11. Coupled with further genetic analyses of the effects of azole and phenothiazine drugs, our data indicate that these compounds are sensed and responded to differentially in the yeast cell.
Etoposide targets 2A protease to inhibit enterovirus 71 replication
Authors: Liang Qinqin , Shi Sai , Zhang Qingjie , Wang Yaxin , Ye Sheng , Xu Binghong
Published: November 2024

Enterovirus 71 (EV71) is a major pathogen that causes hand, foot, and mouth disease (HFMD) in infants and children. Notably, no clinically approved drugs specifically target EV71. The EV71 2A protease (2A
pro
), a cysteine protease produced by the virus, is essential for the virus’ replication and has a significant impact on the functioning of host cells. Thus, it presents a valuable target for the discovery of antiviral medications. In this study, based on the monomers and their derivatives in the Library of Traditional Chinese Medicine (TCM), we performed virtual screening and biological experiments. We identified a derivative of a traditional herbal monomer, Etoposide, commonly isolated from the roots and rhizomes of
Podophyllum
spp. Etoposide inhibited replication of EV71 A, B, C, and CVA16 viruses in a concentration-dependent manner in a variety of cell lines with minimal cytotoxicity. Furthermore, both molecular dynamics simulations and site-directed mutagenesis assays revealed that Etoposide inhibited the activity of the EV71 2A protease by mainly binding to two residues, Y89 and P107. The findings indicate that Etoposide serves as a promising inhibitor of the EV71 2A
pro
, demonstrating strong antiviral properties and positioning itself as a formidable candidate for clinical trials against EV71.

IMPORTANCE

We first used a drug screening approach focused on monomeric compounds and their derivatives from traditional Chinese medicine to identify an EV71 2A
pro
inhibitor—Etoposide. We then performed biological experiments to validate that Etoposide suppresses the replication of the EV71 virus in a concentration-dependent manner with minimal cytotoxicity to various cell lines. Remarkably, it shows inhibitory activity against EV71 A, B, C, and CVA16, suggesting that Etoposide may be a potential broad-spectrum inhibitor. We revealed a novel mechanism that Etoposide inhibits EV71 proliferation by targeting 2A
pro
, and the interactions with Y89 and P107 are of great importance. The findings suggest that Etoposide serves as a promising inhibitor of EV71 2A
pro
, demonstrating significant antiviral properties. It stands out as a strong candidate for broad-spectrum applications in clinical research.
Supplemental Material: Geochronology and provenance of the Huangyangling Formation in the East Kunlun orogen, NW China: Insight from detrital zircon and calcite cement records
Authors: Qi Nan , LI NUO , al. et
Published: November 2024

Tables S1-S3 and Supplemental Data S1. 
Acquired factor V inhibitor treated with rituximab
Authors: Ansari Faisal , Lee Yurhee , Ansari Umar , Kim Phyllis
Published: November 2024

Acquired factor V (FV) inhibitors are extremely rare and present with a broad spectrum ranging from asymptomatic laboratory anomalies to life-threatening critical bleeds. The overall rarity along with the heterogeneity of clinical presentations poses a challenge in diagnosis. There is currently no standard of care immunosuppressive therapy (IST) in these settings. Most patients in the literature receive multiple agents, including but not limited to combinations of IST and/or recombinant products.

Here, we present a case of a man in his 50s who initially presented with oozing at peripheral IV and tracheostomy sites with intermittent epistaxis. He was later found to have an FV activity level of less than 1% and an FV inhibitor titre of 184 Bethesda units/mL. The patient was initially stabilised with fresh frozen plasma, platelets and tranexamic acid and treated with intravenous immunoglobulin and glucocorticoids. However, this resulted in only mild improvement in his coagulation studies. He was then treated with weekly doses of rituximab for 4 weeks with ongoing glucocorticoids without complications. This adds to the growing literature on rituximab as a possible treatment option for acquired FV inhibitors.
Efficacy and acceptability of lurasidone for bipolar depression: a systematic review and dose–response meta-analysis
Authors: Lin Yu-Wei , Chen Yang-Chieh Brian , Hung Kuo-Chuan , Liang Chih-Sung , Tseng Ping-Tao , Carvalho Andre F , Vieta Eduard , Solmi Marco , Lai Edward Chia-Cheng , Lin Pao-Yen , Hsu Chih-Wei , Tu Yu-Kang
Published: November 2024

Question

The optimal dose of lurasidone for bipolar depression is unclear. This study examined its dose–response relationship for efficacy, acceptability, and metabolic/endocrine profiles.

Study selection and analysis

Five databases and grey literature published until 1 August 2024, were systematically reviewed. The outcomes included efficacy (changes in depression, anxiety, clinical global impression, disability and quality of life), acceptability (dropout, manic switch, suicidality and side effects) and metabolic/endocrine profiles (changes in body weight, glucose, lipid and prolactin levels). Effect sizes were calculated using a one-step dose–response meta-analysis, expressed as standardised mean differences (SMDs), risk ratios (RRs) and mean differences (MDs) with 95% CIs.

Findings

Five randomised clinical trials (2032 patients, mean treatment duration 6 weeks) indicated that the optimal therapeutic dose of lurasidone (40–60 mg) improved depression (50 mg: SMD −0.60 (95% CI −0.30, –0.89)), anxiety (50 mg: −0.32 (95% CI −0.21, –0.42)), clinical global impression (50 mg: −0.67 (95% CI −0.30, –1.03)) and disability (50 mg: −0.38 (95% CI −0.08, –0.69)). Side effects increased with higher doses (50 mg: RR 1.15 (95% CI 1.05, 1.25); 100 mg: 1.18 (95% CI 1.02, 1.36)), but dropout, manic switch and suicidality did not show a dose–effect relationship. Weight increased at doses<60 mg (40 mg: MD 0.38 (95% CI 0.16, 0.60) kg), while blood glucose levels rose at doses>70 mg (100 mg: 3.16 (95% CI 0.76, 5.57) mg/dL). Prolactin levels increased in both males (50 mg: 3.21 (95% CI 1.59, 4.84) ng/mL; 100 mg: 5.61 (95% CI 2.42, 8.81)) and females (50 mg: 6.64 (95% CI 3.50, 9.78); 100 mg: 5.33 (95% CI 0.67, 10.00)).

Conclusions

A daily dose of 40–60 mg of lurasidone is a reasonable choice for bipolar depression treatment.

Trial registration number

INPLASY202430069.
Transcatheter aortic valve implantation versus surgical aortic valve replacement in Chinese patients with intermediate and high surgical risk for aortic stenosis: a decision analysis on effect, affordability and cost-effectiveness
Authors: Chen Tongfeng , Gao Chuanyu , Chen Chong , Zhao Yipin , Cheng Jiangtao , Guo Xiaoyan , Hu Dan , Liu Chang , Liu Yuhao
Published: November 2024

Objective

Examine the cost-effectiveness of transcatheter aortic valve implantation (TAVI) versus surgical aortic valve replacement (SAVR) for Chinese patients with severe aortic stenosis (AS) at intermediate and high surgical risk.

Design

A two-phase model, comprising a 1-month decision tree to simulate perioperative outcomes and a 5-year Markov model with monthly cycles to simulate long-term outcomes, has been developed to evaluate the cost-effectiveness of TAVI compared with SAVR for Chinese patients with AS at intermediate and high risk. The event rates for both phases are sourced from the Placement of Aortic Transcatheter Valves IA and IIA trials, while the cost inputs and utility values are sourced from local sources or published literature. Adjustments for inflation were made using consumer price indexes for healthcare to enhance precision. To ensure the reliability and robustness of the model, sensitivity analyses were conducted to assess their impact on outcomes.

Setting

China healthcare system perspective.

Participants

A hypothetical cohort of Chinese patients with AS in intermediate and high surgical risk.

Interventions

TAVI versus SAVR.

Outcome measures

Cost, quality-adjusted life-years (QALYs), life-years gained and incremental cost-effectiveness Ratio (ICER).

Result

For both intermediate- and high-risk AS patients, offering TAVR resulted in high healthcare costs but moderate benefits compared with SAVR. Specifically, in the intermediate-risk population, TAVR led to a 0.34 QALY increase over SAVR, with an incremental cost of $16 707.58, resulting in an ICER of $49 176.60/QALY. Similarly, in the high-risk population, TAVR showed a 0.15 QALY increase over SAVR, with an incremental cost of $18 093.52, leading to an ICER of $122 696.37/QALY. However, both ICERs exceeded the willingness-to-pay threshold of $37 654.50/QALY. Sensitivity analyses confirmed the model’s stability under parameter uncertainty.

Conclusion

TAVI was deemed not cost-effective compared with SAVR for patients with AS at intermediate or high surgical risk in the Chinese healthcare system. Lowering valve costs was considered an effective approach to improve the cost-effectiveness of TAVI.
Uses of private health provider data for governance in low-income and middle-income countries: results from a scoping review
Authors: Faddoul Alix , Montagu Dominic , Kanneganti Sneha , O’Hanlon Barbara
Published: November 2024

This work grew from an interest in understanding how private data are used for health system governance in low-income and middle-income countries (LMICs).

Objective

We conducted a scoping review to understand how the public sector collects routine data from the private health sector and uses it for governance purposes. The private health sector was defined to include both formal and informal, for-profit or non-profit, actors delivering healthcare services.

Findings

We identified 4014 individual English language studies published between 2010 and 2021. We reviewed titles and abstracts of all, with 50% reviewed by two authors to ensure a common application of inclusion criteria. 89 studies were selected for review in full; following this, 26 articles were included in the final selection as they directly report on the use of routine private sector data for governance in LMICs. Only English language studies were included, limiting the scope of possible conclusions.

Results

Data were most commonly collected by the Ministry of Health or a subministerial office, with extraction from District Health Information System 2 specifically cited for three studies. 16 studies collected data on infrastructure and distribution, 15 on service delivery, 12 on health financing, 7 on pharmaceuticals and other consumables, 4 on health workforce, 4 on quality of care and 4 on epidemic surveillance.

Conclusion

The studies identified provide examples of the public sector’s capacity to collect and use data routinely collected from the private sector to perform essential governance functions. The paucity of studies identified is an indication that more attention is needed to ensure that this key area of health system governance is undertaken and that lessons learnt are shared. This review provides insights to understanding private sector health data collection and use for governance in LMICs, and for guiding activities to assess and improve this according to country context and capacity.
Pain during prolonged sitting in subjects with patellofemoral pain in Dutch physical therapy clinics: an online questionnaire-based analysis
Authors: Ophey Martin , Frieling Sophie , Kerkhoffs Gino M M J , Tak Igor
Published: November 2024

Objectives

This study aimed to describe (1) differences between subjects with patellofemoral pain (PFP) with and without pain during prolonged sitting (PDPS), (2) minimum knee flexion angle and time to onset/disappearance of PDPS and (3) differences between those with PDPS at smaller/greater flexion angles and with fast/slow onset and disappearance of PDPS.

Design

Patient-reported online questionnaire.

Setting

Private physical therapy clinics in the Netherlands between May 2021 and March 2023.

Participants

87 participants (61 (70%) females, mean age 22.0 years (IQR 4.0), body mass index 23.1 (4.7)).

Outcome measures

Visual Analogue Scale for worst pain (VAS-W) and sitting pain (VAS-W sitting), the Anterior Knee Pain Scale (AKPS), knee flexion angle to provoke PDPS and time to onset/disappearance of PDPS.

Results

63 of 87 (72%) participants reported PDPS. Participants with PDPS experienced bilateral symptoms of PFP more frequently (71% vs 46%, p=0.44) and scored 12 points lower on the AKPS (p<0.001). Most participants (85%) reported a minimum knee flexion angle of ≥90°, median time to PDPS onset of 16–20 min and 6–10 min for disappearance. Participants experiencing PDPS at smaller flexion angles exhibited higher VAS-W and VAS-W sitting scores (7.0 (1.0), 6.8 (1.1)) than those at greater flexion angles (5.0 (3.0), for both) (p=0.002, p=0.001). Participants with fast onset of PDPS reported higher VAS-W and VAS-W sitting scores (7.0 (2.0), 6.0 (2.0)) than those with slow onset (5.0 (3.0), 5.0 (4.0)) (p<0.001, p=0.025).

Conclusions

Participants with PDPS reported higher levels of disability than those without. PDPS was typically induced at knee flexion of ≥90°, with delayed onset/disappearance. Higher pain levels were reported by those experiencing PDPS at smaller knee flexion angles or with faster onset. Future research should explore the mechanisms of PDPS and develop targeted interventions to improve long-term outcomes.
Consensus definition of a radiologically healed fistula on magnetic resonance imaging in perianal Crohn’s disease: an international Delphi study
Authors: Anand Easan , Devi Jalpa , Joshi Shivani , Antoniou Anna , Doering Michelle , Stoker Jaap , Lung Phillip , Hart Ailsa L , Ballard David H , Deepak Parakkal , Tozer Phil
Published: November 2024

Introduction

Perianal fistulising Crohn’s disease (pfCD) is a distinct and debilitating phenotype seen in around one-third of patients with CD. Clinical trials in pfCD are increasingly using magnetic resonance imaging (MRI) criteria as a primary endpoint, but there is heterogeneity in the radiological definition of a healed perianal fistula that currently limits our ability to perform meaningful meta-analyses of studies. Our aim is to standardise outcomes through the generation of an international consensus definition of a radiologically healed fistula.

Methods and analysis

This international Delphi consensus study employs a two-part strategy.

The first is a systematic review to identify a longlist of variables used to define radiological healing in pfCD. MRI-based indices used to score fistula severity and healing will be assessed for their methodological quality using Consensus-based Standards for the selection of health Measurement Instruments (COSMIN). The systematic review protocol will be conducted using COSMIN methodology and reported using Preferred Reporting Items for Systematic Reviews and Meta-Analyses.

The second part will be an online Delphi consensus, guided by the results of the systematic review. Radiologists, gastroenterologists and colorectal surgeons with expertise in the management of pfCD will be invited to take part in two to three rounds of online surveys. Once an a priori threshold of >80% agreement is reached on individual radiological components used to define ‘healing’ and ‘healed’, a final meeting of key stakeholders will be organised to generate a consensus definition of a healed fistula.

Ethics and dissemination

The study has been deemed exempt from a formal Research Ethics Committee review as no patients will participate directly in the consensus process, given the technical nature of the research question. The study is registered with the local R&D department (Reference RD24/007). Publication of this study will help standardise radiological endpoint measurement in clinical trials of pfCD and improve the synthesis and meta-analysis of comparative studies.

PROSPERO registration number

CRD42024504334.
Managing experts’ conflicts of interest in the EU Joint Clinical Assessment
Authors: Gentilini Arianna , Parvanova Iva
Published: November 2024

Objective

This article critically evaluates the European Commission’s 2024 Implementing Regulation (IR) on conflicts of interest (COIs) management for stakeholders in the European Union (EU) Joint Clinical Assessment (JCA), with a focus on individual experts such as clinicians and patient representatives.

Key findings

The IR is the first EU-level framework to assess COIs in the context of health technology assessment (HTA). The regulation requires experts involved in the JCA to submit annual declarations of interest for both financial and non-financial interests and presents a matrix on whether these conflicts should disqualify them from participating in the joint work. We compared the IR to COIs-management approaches from other European national HTA bodies and found that the IR is closely modelled after the French guidelines. Concerns include potential over-representation of experts from a small number of countries, lack of guidance on organisational COIs, and ambiguities in how the size of financial interests are disclosed. Unclear resource allocation for enforcement could also hinder compliance.

Conclusions

The IR marks progress in EU-wide HTA collaboration, but improvements in transparency, expert diversity, and comprehensive COIs management are needed to ensure impartiality in the JCA process.
Natural killer cells are required for the recruitment of CD8+ T cells and the efficacy of immune checkpoint blockade in melanoma brain metastases
Authors: Fife Christopher , Williams Jennifer , James Fiona , Gregory Scott , Andreou Tereza , Sunderland Ashley , McKimmie Clive , Brownlie Rebecca J , Salmond Robert J , Heaton Samuel , Errington-Mais Fiona , Hadi Zarnaz , Westhead David R , Hall Marlous , Davie Alexander , Emmett Amber , Lorger Mihaela
Published: November 2024

BackgroundBrain metastases (BrM) affect up to 60% of patients with metastatic melanoma and are associated with poor prognosis. While combined immune checkpoint blockade of programmed death-1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) demonstrates intracranial efficacy in a proportion of patients with melanoma, the responses are rarely durable, particularly in patients with symptomatic BrM. The brain is an immune-specialized organ and immune responses are regulated differently to the periphery.

MethodsUsing our previously established two-site model of melanoma BrM with concomitant intracranial and extracranial tumors, in which clinically observed efficacy of the combined PD-1/CTLA-4 (PC) blockade can be reproduced, we here explored the role of natural killer (NK) cells in BrM, using functional studies, immunophenotyping and molecular profiling.

ResultsWe demonstrate that NK cells are required for the intracranial efficacy of PC blockade. While both perforin and interferon gamma were necessary for the PC blockade-dependent control of intracranial tumor growth, NK cells isolated from intracranial tumors demonstrated only a limited cancer cell killing ability, and PC blockade did not alter the abundance of NK cells within tumors. However, the depletion of NK cells in PC blockade-treated mice led to tumor molecular profiles reminiscent of those observed in intracranial tumors that failed to respond to therapy. Furthermore, the depletion of NK cells resulted in a strikingly reduced abundance of CD8+ T cells within intracranial tumors, while the abundance of other immune cell populations including CD4+ T cells, macrophages and microglia remained unaltered. Adoptive T cell transfer experiments demonstrated that PC blockade-induced trafficking of CD8+ T cells to intracranial tumors was chemokine-dependent. In line with this, PC blockade enhanced intratumoral expression of several T cell-attracting chemokines and we observed high expression levels of cognate chemokine receptors on BrM-infiltrating CD8+ T cells in mice, as well as in human BrM. Importantly, the depletion of NK cells strikingly reduced the intratumoral expression levels of T cell attracting chemokines and vascular T cell entry receptors that were upregulated following PC blockade.

ConclusionOur data demonstrate that NK cells underpin the efficacy of PC blockade in BrM by orchestrating the "responder" molecular profile in tumors, and by controlling the intratumoral abundance of CD8+ T cells through regulation of multiple key molecular mediators of T cell trafficking.
Clinical benefit with tebentafusp in a patient with GNAQ mutant metastatic blue nevus-associated melanoma
Authors: Kudelka Matthew R , Richards Allison L , Friedlander Philip , Wolchok Jedd D , Moy Andrea P , Shoushtari Alexander N
Published: November 2024

Melanoma arising in association with a blue nevus (BN) is rare but has molecular similarities to uveal melanoma (UM), including GNAQ/11 mutations. Tebentafusp was recently approved for UM based on improved overall survival in a phase 3 study. We hypothesized that tebentafusp may be active in BN-associated melanoma. Here, we present a case of metastatic BN-associated melanoma with rapid response and ~1 year of disease control on tebentafusp. We also explore molecular and histological features of secondary resistance. Our case highlights that PD-1-resistant melanomas should be screened for GNAQ/11 mutations, as tebentafusp may be a treatment option in this extremely rare disease.
Inhibition of Cbl-b restores effector functions of human intratumoral NK cells
Authors: Tundo Sofia , Trefny Marcel , Rodić Andrijana , Grueninger Olivia , Brodmann Nicole , Börsch Anastasiya , Serger Clara , Fürst Jonas , Buchi Melanie , Buczak Katarzyna , Müller Alex T , Sach-Peltason Lisa , Don Leyla , Herzig Petra , Lardinois Didier , Heinzelmann-Schwarz Viola , Mertz Kirsten D , Hojski Aljaž , Schaeuble Karin , Laubli Heinz , Natoli Marina , Toso Alberto , Luu Thuy T , Zippelius Alfred , Romagnani Andrea
Published: November 2024

Background

T cell-based immunotherapies including immune checkpoint blockade and chimeric antigen receptor T cells can induce durable responses in patients with cancer. However, clinical efficacy is limited due to the ability of cancer cells to evade immune surveillance. While T cells have been the primary focus of immunotherapy, recent research has highlighted the importance of natural killer (NK) cells in directly recognizing and eliminating tumor cells and playing a key role in the set-up of an effective adaptive immune response. The remarkable potential of NK cells for cancer immunotherapy is demonstrated by their ability to broadly identify stressed cells, irrespective of the presence of neoantigens, and their ability to fight tumors that have lost their major histocompatibility complex class I (MHC I) expression due to acquired resistance mechanisms.

However, like T cells, NK cells can become dysfunctional within the tumor microenvironment. Strategies to enhance and reinvigorate NK cell activity hold potential for bolstering cancer immunotherapy.

Methods

In this study, we conducted a high-throughput screen to identify molecules that could enhance primary human NK cell function. After compound validation, we investigated the effect of the top performing compounds on dysfunctional NK cells that were generated by a newly developed in vitro platform. Functional activity of NK cells was investigated using compounds alone and in combination with checkpoint inhibitor blockade. The findings were validated on patient-derived intratumoral dysfunctional NK cells from different cancer types.

Results

The screening approach led to the identification of a Casitas B-lineage lymphoma (Cbl-b) inhibitor enhancing the activity of primary human NK cells. Furthermore, the Cbl-b inhibitor was able to reinvigorate the activity of in vitro generated and patient-derived dysfunctional NK cells. Finally, Cbl-b inhibition combined with T-cell immunoreceptor with Ig and ITIM domains (TIGIT) blockade further increased the cytotoxic potential and reinvigoration of both in vitro generated and patient-derived intratumoral dysfunctional NK cells.

Conclusions

These findings underscore the relevance of Cbl-b inhibition in overcoming NK cell dysfunctionality with the potential to complement existing immunotherapies and improve outcomes for patients with cancer.
Adoptive transfer of membrane-restricted IL-12-TCR T cells promotes antigen spreading and elimination of antigen-negative tumor variants
Authors: Zhang Ling , Norberg Scott M , Karimipour Farrah , Davies John S , Kuznetsov Alex , Lassoued Wiem , Burnett Daniel , Homan Philip , Cam Margaret , Sinkoe Andrew , Xue Ping , Gulley James L , Hinrichs Christian S
Published: November 2024

Background

Adoptive T-cell therapy has demonstrated clinical activity in B-cell malignancies, offering hope for its application to a broad spectrum of cancers. However, a significant portion of patients with solid tumors experience primary or secondary resistance to this treatment modality. Target antigen loss resulting either from non-uniform antigen expression or defects in antigen processing and presentation machinery is one well-characterized resistance mechanism. Constitutively expressed membrane-anchored interleukin-12 (caIL-12) has demonstrated enhanced antitumor activity and low systemic exposure in multiple preclinical adoptive T-cell treatment models with homogeneous tumor antigen expression. In this study, we assess the therapeutic impact of caIL-12 on target antigen-negative variants in syngeneic mouse models.

Methods

Target antigen-positive tumors were generated by transducing B16F10 melanoma cells (B16) or Lewis Lung Carcinoma cells (LLC) with a construct expressing the OVA antigen, SIINFEKL, tagged to ubiquitin (B16-U-OVA, LLC-U-OVA), while B16 or LLC tumors served as antigen-negative variants. C57BL/6J mice were subcutaneously injected with heterogeneous tumors composed of 80% B16-U-OVA and 20% B16. Bilateral tumors were established by injecting the left flank with B16-U-OVA or LLC-U-OVA tumors and the right flank injected with B16 or LLC tumors. The tumor-bearing mice then underwent 5.5 Gy total body irradiation, followed by adoptive transfer of OT-I TCR-T cells engineered with or without caIL-12.

Results

TCR-T cells (OT-I) delivered caIL-12 to the B16-U-OVA tumor sites and induced robust tumor control and survival benefits in mice bearing a heterogeneous tumor with OVA-negative variants. caIL-12 exerted its effect on OVA-negative B16 variants primarily by priming and activating endogenous antitumor CD8 T cells via antigen spreading. In addition, antigen spreading induced by OT-I-caIL-12 resulted in controlling OVA-negative tumors implanted at distant sites. This therapeutic effect required antigen-specific TCR-T cells and caIL-12 to colocalize at the tumor site, along with endogenous CD8 T cells capable of recognizing shared tumor antigens.

Conclusion

Expression of caIL-12 by tumor-targeting T cells demonstrated therapeutic effect against target-antigen-negative tumor variants, primarily through the induction of antigen spreading. These findings highlight the potential of caIL-12 to address challenges of antigen escape and tumor heterogeneity that may limit the efficacy of T-cell therapy against solid tumors.
Afatinib boosts CAR-T cell antitumor therapeutic efficacy via metabolism and fate reprogramming
Authors: Dai Yueyu , Liu Yue , An Lingna , Zhong Fangyuan , Zhang Xi , Lou Shifeng
Published: November 2024

Background

Chimeric antigen receptor T (CAR-T) cell therapy has been shown remarkable efficacy in the treatment of hematological malignancies in recent years. However, a considerable proportion of patients would experience tumor recurrence and deterioration. Insufficient CAR-T cell persistence is the major reason for relapse. Multiple strategies to enhance the long-term antitumor effects of CAR-T cells have been explored and developed. In this study, we focused on tyrosine kinase inhibitors (TKIs), which have emerged immunomodulatory potential besides direct tumoricidal effects.

Methods

Here, we screened 50 approved TKIs drugs and identified that afatinib (AFA) markedly enhanced the expressing of CD62L and inhibited reactive oxygen species level in T cells. And the underlying mechanisms of AFA medicating T cells were explored by detecting signal transduction, and metabolism pattern. Furthermore, we co-cultured AFA with CAR-T cells during the preparation stage and multianalyses of differentiation characteristics, metabolic profiling, and RNA sequencing revealed that AFA induce comprehensive metabolism remodeling and fate reprogramming. Based on it, we finally identified the antitumor efficacy of AFA-pretreatment CAR-T compared with negative-control CAR-T.

Results

We identified that AFA blocked the T-cell receptor (TCR) and phosphoinositide 3-kinase-protein kinase B-mechanistic target of rapamycin signaling pathways, induced metabolic reprogramming and modulated T-cell differentiation. When combined with CAR-T cells, AFA inhibited the exhaustion and enhanced the persistence and cytotoxicity. Our results revealed that the pretreatment of AFA enables to boost CAR-T cells with strong antitumor cytotoxicity in leukemia mouse model.

Conclusions

Our study systematically demonstrated that AFA pretreatment effectively enhanced CAR-T cells antitumor performance, which presents a novel optimization strategy for potent and durable CAR-T cell therapy.
Gut microbiota in very early systemic sclerosis: the first case-control taxonomic and functional characterisation highlighting an altered butyric acid profile
Authors: Bellando-Randone Silvia , Russo Edda , Di Gloria Leandro , Lepri Gemma , Baldi Simone , Fioretto Bianca Saveria , Romano Eloisa , Ghezzi Giulio , Bertorello Sara , El Aoufy Khadija , Rosa Irene , Pallecchi Marco , Bruni Cosimo , Cei Francesco , Nannini Giulia , Niccolai Elena , Orlandi Martina , Bandini Giulia , Guiducci Serena , Bartolucci Gian Luca , Ramazzotti Matteo , Manetti Mirko , Matucci-Cerinic Marco , Amedei Amedeo
Published: November 2024

Objectives

In systemic sclerosis (SSc), gastrointestinal involvement is one of the earliest events. We compared the gut microbiota (GM), its short-chain fatty acids (SCFAs) and host-derived free fatty acids (FFAs) in patients with very early diagnosis of SSc (VEDOSS) and definite SSc.

Methods

Stool samples of 26 patients with SSc, 18 patients with VEDOSS and 20 healthy controls (HC) were collected. The GM was assessed through 16S rRNA sequencing, while SCFAs and FFAs were assessed by gas chromatography-mass spectrometry.

Results

In patients with VEDOSS, an increase in Bacteroidales and Oscillospirales orders and a decrease in Bacilli class,Blautia, Romboutsia, StreptococcusandTuricibactergenera was detected in comparison with HC. In patients with SSc, an elevated number of Acidaminococcaceae and Sutterellaceae families, along with a decrease of the Peptostreptococcaceae family andAnaerostipes, Blautia, RomboutsiaandTuricibactergenera was found in comparison with HC. Patients with SSc and VEDOSS had a significantly lower butyrate and higher acetate with respect to HC. In VEDOSS, an increase in Oscillospiraceae family andAnaerostipesgenus, and a decrease inAlphaproteobacteriaclass, and Lactobacillales order was identified with respect to SSc. Moreover, patients with VEDOSS exhibited higher acetate and lower valerate compared with definite SSc.

Conclusion

A GM dysbiosis with depletion of beneficial anti-inflammatory bacteria (especially butyrate-producing) and a significant decrease in faecal butyrate was identified in patients with VEDOSS. This early GM imbalance may foster the growth of inflammatory microbes, worsening intestinal dysbiosis and inflammation in early SSc stages. The potential butyrate administration in early disease phases might be considered as a novel therapeutic approach to mitigate gastrointestinal discomfort and progression preserving patient’s quality of life.
Fibroblast-like synoviocyte targeting antibodies are associated with failure to reach early and sustained remission or low disease activity after first-line therapy in rheumatoid arthritis
Authors: Vandormael Patrick , Fadlallah Sukayna , Ruytinx Pieter , Pues Astrid , Sleurs Ellen , Liesenborgs Jori , Joly Johan , Agten Anouk , Vandenabeele Frank , Fraussen Judith , Verschueren Patrick , Somers Veerle
Published: November 2024

Objective

To discover antibody biomarkers that can predict a lack of response to first-line therapy in rheumatoid arthritis (RA) patients.

Methods

Two RA cDNA phage display libraries were screened for novel antibodies in baseline RA sera from the Care in early RA (CareRA) trial, differentiating between patients who did or did not reach remission after first-line therapy (n=20 each). Antibody reactivity to identified University Hasselt (UH)-RA antigens was validated in baseline samples from 136 additional CareRA participants. The novel antibodies’ potential to predict failure to reach remission or low disease activity (LDA), according to the Disease Activity Score 28-joint C-reactive protein/erythrocyte sedimentation rate (DAS28CRP/ESR) and Clinical/Simplified Disease Activity Index (CDAI/SDAI), was studied by multivariate analyses. The presence of the antibody targets in RA synovial tissue and the fibroblast-like synoviocyte (FLS) cell line SW982 was determined by immunofluorescence.

Results

We identified antibodies to 41 novel antigens. Antibodies against any of three antigens, UH-RA.305/318/329, discriminated between RA patients not reaching week (w)8 DAS28CRP remission and those that did (36% vs 13%,p=0.0031). In all patients, anti-UH-RA.305/318/329 antibody reactivity was associated with failure to reach week 8 DAS28CRP and DAS28ESR remission (OR 3.63,p=0.0031; OR 2.92,p=0.016; respectively), SDAI/CDAI sustained remission (OR 5.59,p=0.039 for both) and DAS28CRP and DAS28ESR sustained LDA (OR 3.7,p=0.009; OR 2.76,p=0.042; respectively). In rheumatoid factor/anti-citrullinated protein antibody (RF/ACPA) seronegative patients, these antibodies were strongly associated with failure to achieve week 8 DAS28CRP remission (OR 17.3,p=0.0029). Anti-UH-RA.305/329 antibodies were shown to target FLS in RA synovial tissue and SW982 cells.

Conclusion

We identified three antibody biomarkers that are associated with failure to achieve remission/LDA after first-line RA therapy.