bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning security and privacy: a review of threats and countermeasures
Authors: Paracha Anum , Arshad Junaid , Farah Mohamed Ben , Ismail Khalid 
Published: April 2024

AbstractMachine learning has become prevalent in transforming diverse aspects of our daily lives through intelligent digital solutions. Advanced disease diagnosis, autonomous vehicular systems, and automated threat detection and triage are some prominent use cases. Furthermore, the increasing use of machine learning in critical national infrastructures such as smart grids, transport, and natural resources makes it an attractive target for adversaries. The threat to machine learning systems is aggravated due to the ability of mal-actors to reverse engineer publicly available models, gaining insight into the algorithms underpinning these models. Focusing on the threat landscape for machine learning systems, we have conducted an in-depth analysis to critically examine the security and privacy threats to machine learning and the factors involved in developing these adversarial attacks. Our analysis highlighted that feature engineering, model architecture, and targeted system knowledge are crucial aspects in formulating these attacks. Furthermore, one successful attack can lead to other attacks; for instance, poisoning attacks can lead to membership inference and backdoor attacks. We have also reviewed the literature concerning methods and techniques to mitigate these threats whilst identifying their limitations including data sanitization, adversarial training, and differential privacy. Cleaning and sanitizing datasets may lead to other challenges, including underfitting and affecting model performance, whereas differential privacy does not completely preserve model’s privacy. Leveraging the analysis of attack surfaces and mitigation techniques, we identify potential research directions to improve the trustworthiness of machine learning systems.
Severe enduring anorexia nervosa (SE-AN) treatment options and their effectiveness: a review of literature
Authors: Marcolini Federica , Ravaglia Alessandro , Tempia Valenta Silvia , Bosco Giovanna , Marconi Giorgia , De Ronchi Diana , Atti Anna Rita 
Published: April 2024

Abstract
Introduction
For nearly 20% of patients diagnosed with Anorexia Nervosa (AN), the eating disorder (ED) is prolonged and becomes long-lasting. It has been reported that patients diagnosed with Severe Enduring Anorexia Nervosa (SE-AN) have worse ED symptoms, higher rates of lifetime hospitalization, and lower psychosocial well-being compared to patients with shorter disease duration.

Objectives
This review aims to describe the treatments proposed to date and their effectiveness on SE-AN-related outcomes.

Methods
We conducted a PubMed search for studies addressing the issue of treatment approach to SE-AN adults, that were published between 2003 and 2023, peer-reviewed, written in the English language, and available in full-text. Next, we inductively created relevant macro-themes by synthesizing the data from the included articles.

Results
Of 251 PubMed studies, 25 articles were considered for data extraction, all published between 2003 and 2022. We identified three macro-themes. The first macro-theme, “Psychotherapy”, mostly takes into consideration treatment effectiveness of cognitive behavioral therapy (CBT). Various reports determined its greater effectiveness compared to Specialist Supportive Clinical Management (SSCM), and one study proved that outpatient CBT is a valid alternative to hospitalization. The second one involves “Pharmacological Treatments”. Research on dronabinol, a synthetic orexigenic cannabinoid, antipsychotics (in particular, olanzapine and haloperidol), and ketamine showed some mixed results regarding the often-complementary areas of weight gain and improvement in ED-related symptoms. Regarding the third macro-theme, “Brain Stimulation Therapies,” such as Repetitive Transcranial Magnetic Stimulation (rTMS) and Deep Brain Stimulation (DBS), we found promising results in improving ED-related psychological traits (such as mood and anxiety), affective regulation, and quality of life. However, we have observed divergent results regarding outcome measures such as BMI and weight gain.

Conclusions
SE-AN patients are predicted to encounter both medical complications and psychological distress of increasing severity that will inevitably affect their quality of life; to our knowledge, research evidence on treatment options for SE-AN remains limited, and the methodological quality of studies is generally low. These findings denote the need to focus future research efforts on effective treatment strategies specific to long-lasting EDs.
MicroRNAs predict early complications of autologous hematopoietic stem cell transplantation
Authors: Mikulski Damian , Nowicki Mateusz , Dróżdż Izabela , Perdas Ewelina , Strzałka Piotr , Kościelny Kacper , Misiewicz Małgorzata , Stawiski Konrad , Wierzbowska Agnieszka , Fendler Wojciech 
Published: April 2024

AbstractAutologous hematopoietic stem cell transplantation (AHSCT) remains the most prevalent type of stem cell transplantation. In our study, we investigated the changes in circulating miRNAs in AHSCT recipients and their potential to predict early procedure-related complications. We collected serum samples from 77 patients, including 54 with multiple myeloma, at four key time points: before AHSCT, on the day of transplantation (day 0), and at days + 7 and + 14 post-transplantation. Through serum miRNA-seq analysis, we identified altered expression patterns and miRNAs associated with the AHSCT procedure. Validation using qPCR confirmed deviations in the levels of miRNAs at the beginning of the procedure in patients who subsequently developed bacteremia: hsa-miR-223-3p and hsa-miR-15b-5p exhibited decreased expression, while hsa-miR-126-5p had increased level. Then, a neural network model was constructed to use miRNA levels for the prediction of bacteremia. The model achieved an accuracy of 93.33% (95%CI: 68.05-99.83%), with a sensitivity of 100% (95%CI: 67.81-100.00%) and specificity of 90.91% (95%CI: 58.72-99.77%) in predicting bacteremia with mean of 6.5 ± 3.2 days before occurrence. In addition, we showed unique patterns of miRNA expression in patients experiencing platelet engraftment delay which involved the downregulation of hsa-let-7f-5p and upregulation of hsa-miR-96-5p; and neutrophil engraftment delay which was associated with decreased levels of hsa-miR-125a-5p and hsa-miR-15b-5p. Our findings highlight the significant alterations in serum miRNA levels during AHSCT and suggest the clinical utility of miRNA expression patterns as potential biomarkers that could be harnessed to improve patient outcomes, particularly by predicting the risk of bacteremia during AHSCT.
Immune escape of multiple myeloma cells results from low miR29b and the ensuing epigenetic silencing of proteasome genes
Authors: Leone Patrizia , Malerba Eleonora , Prete Marcella , Solimando Antonio Giovanni , Croci Giorgio Alberto , Ditonno Paolo , Tucci Marco , Susca Nicola , Derakhshani Afshin , Dufour Antoine , De Re Valli , Silvestris Nicola , Racanelli Vito 
Published: April 2024

Abstract
Background
Activation of CD28 on multiple myeloma (MM) plasma cells, by binding to CD80 and CD86 on dendritic cells, decreases proteasome subunit expression in the tumor cells and thereby helps them evade being killed by CD8+ T cells. Understanding how CD28 activation leads to proteasome subunit downregulation is needed to design new MM therapies.

Methods
This study investigates the molecular pathway downstream of CD28 activation, using an in vitro model consisting of myeloma cell lines stimulated with anti-CD28-coated beads.

Results
We show that CD28 engagement on U266 and RPMI 8226 cells activates the PI3K/AKT pathway, reduces miR29b expression, increases the expression of DNA methyltransferase 3B (DNMT3B, a target of miR29b), and decreases immunoproteasome subunit expression. In vitro transfection of U266 and RPMI 8226 cells with a miR29b mimic downregulates the PI3K/AKT pathway and DNMT3B expression, restores proteasome subunit levels, and promotes myeloma cell killing by bone marrow CD8+ T cells from MM patients. Freshly purified bone marrow plasma cells (CD138+) from MM patients have lower miR29b and higher DNMT3B (mRNA and protein) than do cells from patients with monoclonal gammopathy of undetermined significance. Finally, in MM patients, high DNMT3B levels associate with shorter overall survival.

Conclusions
Altogether, this study describes a novel molecular pathway in MM. This pathway starts from CD28 expressed on tumor plasma cells and, through the PI3K-miR29b-DNMT3B axis, leads to epigenetic silencing of immunoproteasome subunits, allowing MM plasma cells to elude immunosurveillance. This discovery has implications for the design of innovative miR29b-based therapies for MM.
Systematic analysis of multi-omics data reveals component-specific blood-based biomarkers for Parkinson’s disease
Authors: Tng Teddy J. W. , Wong Barbara Wing Yan , Sim Esther H. Y. , Tan Eng King , Goh Wilson W. B. , Lim Kah-Leong 
Published: April 2024

AbstractParkinson’s disease (PD) is a prevalent neurodegenerative disorder affecting millions of elderly individuals worldwide. Clinically, PD is diagnosed based on the presentation of motoric symptoms. Other methods such as F-DOPA PET scan or α-Synuclein detection from the cerebral spinal fluid are either too expensive or invasive for routine use. Omics platforms such as transcriptomics, proteomics, and metabolomics may identify PD biomarkers from blood, which can reduce cost and increase efficiency. However, there are many biological moieties being measured and issues with false positives/negatives. It is also unknown which omics platform offers most useful information. Therefore, it is important to assess the reliability of these omics studies. Here, we shortlisted and analysed nearly 80 published reports across transcriptomics, proteomics and metabolomics in search of overlapping blood-based biomarkers for PD. The top biomarkers were reported across 29%, 42% and 12.5% of shortlisted papers in transcriptomics, proteomics and metabolomics respectively. These percentages increased to 42%, 60% and 50% accordingly when studies were grouped by specific blood subtypes for analysis, demonstrating the need for test kits to be blood-subtype specific. Following systematic analyses, we propose six novel PD biomarkers: two mRNAs (Whole blood, WB) – Arg1 and SNCA, two proteins (Plasma EV) – SNCA and APOA1, and two metabolites (WB) – 8-OHdG and uric acid for further validation. While these proposed biomarkers are useful, they are also snapshots, representing subsets of larger pathways of origin where the different omics levels corroborate. Indeed, identifying the interconnections across different biological layers can strengthen contextual reasoning, which in turn, would give rise to better quality biomarkers. Knowledge integration across the omics spectrum revealed consistent aberrations on the same neuroinflammation pathway, showcasing the value of integrative (i)-omics agreements for increasing confidence of biomarker selection. We believe that our findings could pave the way for identifying reproducible PD biomarkers, with potential for clinical deployment.
Graphical Abstract
Six Proposed blood-based biomarkers. Seventy-nine publications across transcriptomics, proteomics and metabolomics were shortlisted and analysed for reported biomarkers. The proposed biomarkers are SNCA, APOA1, Arg1, 8-OHdG and Uric acid.
The impact of face coverings on audio-visual contributions to communication with conversational speech
Authors: Jackson I. R. , Perugia E. , Stone M. A. , Saunders G. H. 
Published: April 2024

AbstractThe use of face coverings can make communication more difficult by removing access to visual cues as well as affecting the physical transmission of speech sounds. This study aimed to assess the independent and combined contributions of visual and auditory cues to impaired communication when using face coverings. In an online task, 150 participants rated videos of natural conversation along three dimensions: (1) how much they could follow, (2) how much effort was required, and (3) the clarity of the speech. Visual and audio variables were independently manipulated in each video, so that the same video could be presented with or without a superimposed surgical-style mask, accompanied by one of four audio conditions (either unfiltered audio, or audio-filtered to simulate the attenuation associated with a surgical mask, an FFP3 mask, or a visor). Hypotheses and analyses were pre-registered. Both the audio and visual variables had a statistically significant negative impact across all three dimensions. Whether or not talkers’ faces were visible made the largest contribution to participants’ ratings. The study identifies a degree of attenuation whose negative effects can be overcome by the restoration of visual cues. The significant effects observed in this nominally low-demand task (speech in quiet) highlight the importance of the visual and audio cues in everyday life and that their consideration should be included in future face mask designs.
Desirable and realistic futures of the university: a mixed-methods study with teachers in Denmark
Authors: Pischetola Magda , Stenalt Maria Hvid , Nøhr Liv , Hagood Danielle Elizabeth , Misfeldt Morten 
Published: April 2024

AbstractIn this paper, we put in dialogue the local dimension of a nation-state with the global challenges faced by universities worldwide. We focus on the case of Denmark, a nation that was exceptionally active in implementing international university reforms and where digitalisation is a high priority of the public sector governance. The article seeks to contribute to speculative research and critical studies by presenting a mixed-methods study that explores higher education teachers’ views about desirable and realistic future scenarios in Denmark. The study draws on data from a survey applied at a large Danish university, analysed both quantitatively (N = 755) and qualitatively (N = 53). The findings show that teachers share clusters of concern about uncontrolled digitalisation and teaching automation, commodification of education, and modularisation of university courses, the latter being a contested but realistic perspective in the latest political reforms. They reaffirm the mission of the university as preparing students for solving real problems and contributing to the challenges of the present time. The paper concludes with a call for university management to recalibrate future imaginaries to the values expressed by the teachers, and the university they wish to create.
Biological control potential of two Beauveria bassiana isolates against the stink bugs Nezara viridula L. and Piezodorus guildinii Westwood (Hemiptera: Pentatomidae) in common bean
Authors: Ramos Yordanys , Portal Orelvis , Meyling Nicolai V. , Klingen Ingeborg 
Published: April 2024

Abstract
Background
The stink bugs, Nezara viridula L. and Piezodorus guildinii Westwood (Hemiptera: Pentatomidae) are the most important and widespread species of polyphagous stink bugs in the tropical and subtropical regions of Latin America, which affect the quality and yield of the common bean (Phaseolus vulgaris L.). The use of synthetic chemical insecticides is the major control strategy to manage stink bugs in common beans and alternatives are needed. In this study, mortality and median Lethal Time (LT50) of two Cuban isolates of the entomopathogenic fungus Beauveria bassiana (18 S-O-R and 96 P-O-E), as well as one commercial Cuban isolate (Bb-18), at a concentration of 1 × 108 conidia/ml were evaluated. These evaluations were conducted against both stink bug species using Petri dish bioassays and a semi-field experiment in common beans.

Results
In Petri dish bioassays, the isolates 18 S-O-R and 96 P-O-E caused 100% mortality of both N. viridula and P. guildinii. This was significantly higher than for isolate Bb-18, which caused 86.3% N. viridula and 81.3% P. guildinii mortality. In the semi-field experiment, when pooling both stink bug species, total mortality after 14 days was 91.3% for 18 S-O-R, 80.0% for 96 P-O-E and 73.8% for Bb-18 isolates. LT50 value for isolate 18 S-O-R tested under laboratory conditions was 6.04 ± 0.18 days for N. viridula and 5.32 ± 0.14 days for P. guildinii at the same concentration of 1 × 108 conidia/ml. LT50 value for isolate 18 S-O-R in semi field was 6.79 ± 0.37 days for N. viridula and 7.71 ± 0.32 days for P. guildinii at 1 × 108 conidia/ml.

Conclusion
The study highlights the potential of B. bassiana 18 S-O-R as a promising candidate for control of stink bugs in common bean under tropical conditions as an alternative to conventional chemical insecticides in integrated pest management (IPM) programs. Moving forward, further research should focus on validating the efficacy under diverse field conditions and integrating application methods into practical IPM approaches. Future use of B. bassiana will enhance sustainability and reduce environmental impacts associated with pesticide use.
PeNAC67-PeKAN2-PeSCL23 and B-class MADS-box transcription factors synergistically regulate the specialization process from petal to lip in Phalaenopsis equestris
Authors: Xu Qingyu , Yang Zhenyu , Jia Yupeng , Wang Rui , Zhang Qiyu , Gai Ruonan , Wu Yiding , Yang Qingyong , He Guoren , Wu Ju Hua , Ming Feng 
Published: April 2024

AbstractThe molecular basis of orchid flower development involves a specific regulatory program in which MADS-box transcription factors play a central role. The recent ‘perianth code’ model hypothesizes that two types of higher-order heterotetrameric complexes, namely SP complex and L complex, play pivotal roles in the orchid perianth organ formation. Therefore, we explored their roles and searched for other components of the regulatory network.Through the combined analysis for transposase-accessible chromatin with high-throughput sequencing and RNA sequencing of the lip-like petal and lip from Phalaenopsis equestris var.trilip, transcription factor-(TF) genes involved in lip development were revealed. PeNAC67 encoding a NAC-type TF and PeSCL23 encoding a GRAS-type TF were differentially expressed between the lip-like petal and the lip. PeNAC67 interacted with and stabilized PeMADS3, which positively regulated the development of lip-like petal to lip. PeSCL23 and PeNAC67 competitively bound with PeKAN2 and positively regulated the development of lip-like petal to petal by affecting the level of PeMADS3. PeKAN2 as an important TF that interacts with PeMADS3 and PeMADS9 can promote lip development. These results extend the ‘perianth code’ model and shed light on the complex regulation of orchid flower development.
Approach to the Patient: Concept and Application of Targeted Radiotherapy in the Paraganglioma Patient
Authors: Pacak Karel , Taieb David , Lin Frank I , Jha Abhishek 
Published: April 2024

Abstract
Paragangliomas can metastasize, posing potential challenges both in symptomatic management and disease control. Systemic targeted radiotherapies using 131I-MIBG and 177Lu-DOTATATE are a mainstay in the treatment of metastatic paragangliomas. This clinical scenario and discussion aim to enhance physicians’ knowledge of the stepwise approach to treat these patients with paraganglioma-targeted radiotherapies. It comprehensively discusses current approaches to selecting paraganglioma patients for targeted radiotherapies and how to choose between the two radiotherapies based on specific patient and tumor characteristics, when either therapy is feasible, or one is superior to another. The safety, efficacy, toxicity profiles, and optimization of these radiotherapies are also discussed, along with other therapeutic options including radiotherapies, available for patients besides these two therapies. Perspectives in radiotherapies of paraganglioma patients are outlined since they hold promising approaches in the near future that can improve patient outcomes.
Adrenocortical Adenoma With Protrusion Into the Inferior Vena Cava Initially Suspected to Be Adrenocortical Carcinoma
Authors: Takizawa Hiroki , Higuchi Reo , Fukumura Yuki , Terasawa Muga , Sano Katsuhiro , Goto Hiromasa 
Published: April 2024

Abstract
Adrenal tumors with invasion into the inferior vena cava (IVC) are typically malignant. Here, we present a case of adrenocortical adenoma with protrusion into the IVC. A 70-year-old man was referred to our hospital after his magnetic resonance imaging scan of the abdomen coincidently revealed a right adrenal tumor invading the IVC. We suspected an aggressive adrenal carcinoma and tumor resection was performed. However, all 3 existing pathological criteria (Weiss, modified Weiss, and Helsinki) suggested the tumor was benign. Immunohistochemistry for CD31 showed the tumor inside the central adrenal vein (CAV), right adrenal vein (RAV), and IVC was entirely covered with CD31-positive vascular endothelial cells. The CAV is known to sometimes lack smooth muscle in its walls and normal adrenocortical cells covered by endothelial cells sometimes protrude into the CAV from this gap. These findings suggest that this tumor likely protruded into the IVC by pushing against the CAV wall, rather than by invasion into the vascular wall. In the case with adrenal tumors protruding into the IVC, the fact that the tumor surface was covered by vascular endothelial cells was considered supportive of its benign nature.
Next-Generation Sequencing in Sporadic Medullary Thyroid Cancer Patients: Mutation Profile and Disease Aggressiveness
Authors: Shirali Aditya S , Hu Mimi I , Chiang Yi-Ju , Graham Paul H , Fisher Sarah B , Sosa Julie Ann , Perrier Nancy , Brown Spandana , Holla Vijaykumar R , Dadu Ramona , Busaidy Naifa , Sherman Steven I , Cabanillas Maria , Waguespack Steven G , Zafereo Mark E , Grubbs Elizabeth G 
Published: April 2024

Abstract

Context
Next-generation sequencing (NGS) analysis of sporadic medullary thyroid carcinoma (sMTC) has led to increased detection of somatic mutations, including RET M918T, which has been considered a negative prognostic indicator.

Objective
This study aimed to determine the association between clinicopathologic behavior and somatic mutation identified on clinically motivated NGS.

Methods
In this retrospective cohort study, patients with sMTC who underwent NGS to identify somatic mutations for treatment planning were identified. Clinicopathologic factors, time to distant metastatic disease (DMD), disease-specific survival (DSS), and overall survival (OS) were compared between somatic mutations.

Results
Somatic mutations were identified in 191 sMTC tumors, including RET M918T (53.4%), other RET codons (10.5%), RAS (18.3%), somatic RET indels (8.9%), and RET/RAS wild-type (WT) status (8.9%). The median age at diagnosis was 50 years (range, 11-83); 46.1% were female. When comparing patients with RET M918T, RET-Other, and RET WT (which included RAS and RET/RAS WT), there were no differences in sex, TNM category, systemic therapy use, time to DMD, DSS, or OS. On multivariate analysis, older age at diagnosis (HR 1.05, P &lt; .001; HR 1.06, P&lt; .001) and M1 stage at diagnosis (HR 3.17, P = .001; HR 2.98, P = .001) were associated with decreased DSS and OS, respectively, but mutation cohort was not. When comparing RET M918T to RET indels there was no significant difference in time to DMD, DSS, or OS between the groups.

Conclusion
Somatic RET mutations do not portend compromised DSS or OS in a cohort of sMTC patients who underwent clinically motivated NGS.