Miracle-dz/UniFAR-FTUs huggingface dataset:
Pre-and post-quantum Diﬀie-Hellman from groups, actions, and isogenies

Diﬃe–Hellman key exchange is at the foundations of public-key cryptography, but conventional group-based Diﬃe–Hellman is vulnerable to Shor’s quantum algorithm. A range of “post-quantum Diﬃe– Hellman” protocols have been proposed to mitigate this threat, including the Couveignes, Rostovtsev–Stolbunov, SIDH, and CSIDH schemes, all based on the combinatorial and number-theoretic structures formed by isogenies of elliptic curves. Pre-and post-quantum Diﬃe–Hellman schemes resemble each other at the highest level, but the further down we dive, the more diﬀerences emerge—diﬀerences that are critical when we use Diﬃe–Hellman as a basic component in more complicated constructions. In this survey we compare and contrast pre-and post-quantum Diﬃe–Hellman algorithms, highlighting some important subtleties.
PTMVision: An Interactive Visualization Platform for Post-Translational Modifications of Proteins

In recent years, proteins have been shown to carry many more post-translational modifications (PTMs) than originally thought. The visualization of proteins along with their PTMs facilitates exploration and understanding of the effects of these PTMs on the protein structure, function, and interactions with other proteins. Therefore, we developed PTMVision , an interactive web-based visualization. We combine information about PTMs in the primary sequence with a two-dimensional representation of the protein’s tertiary structure using a presence-absence map and a modified contact map that relates PTMs with the spatial arrangement of proteins without the need of a 3D structure. The prototype of PTMVision is part of the TueVis Visualization Server and is available at https://ptmvision-tuevis.cs. uni-tuebingen.
Identiﬁcation and Characterization of Enterococcus Species Isolated from Forage Crops and Their Inﬂuence on Silage Fermentation

Forty-eight strains of lactic acid bacteria were isolated from forage crops, and their identiﬁcation, characterization and inﬂuence on silage fermentation were studied. All isolates were Gram-positive, short-chain-forming, catalase-negative, and facultatively anaerobic cocci that did not produce gas from glucose, only formed L-lactic acid, and were able to grow at pH 9.6, in 6.5% NaCl, or with 40% bile, but not below pH 4.5. These isolates were commonly isolated from forage crops, and they were divided into four groups (A, B, C, and D) according to sugar fermentation characteristics. Selected strains of FA 5, FA 27, FA 45, and FA 57 were identiﬁed as Enterococcus hirae , E. faecalis , E. casseliﬂavus , and E. mundtii , respectively, on the basis of DNA-DNA homology. Strains FA 5, FA 27, FA 45, and FA 57 and two strains from commercial inoculants, LC 10 ( Lactobacillus casei ) and LP 15 ( L. plantarum ), were used as additives to alfalfa and guinea grass silages. Alphalfa and guinea grass si-lages inoculated with LC 10, LP 15, FA 5+LC 10, and FA 5+LP 15-treatments in alfalfa and guinea grass si-lages had signiﬁcantly lower pH values, contents of butyric acid and ammonia nitrogen, gas production, and dry matter losses compared with the control silage after 60 d of fermentation. However, the E. hirae FA 5, E. faecalis FA 27, E. casseliﬂavus FA 45, and E. mundtii FA 57-inoculated silages gave similar values to the control in both types of silage. The FA 27+LC 10 and FA 27+LP 15-inoculated silages did not differ in fermentation quality from LC 10 and LP 15-inoculated silages alone. The results conﬁrmed that Enterococcus species were not able to improve silage quality.
Biotechnology and Bioengineering

Correspondence John M. Tarbell, PhD, Department of Biomedical Engineering, The City College of New York, CUNY, 160 Convent Avenue, New York, NY 10031. Email: jtarbell@ccny.cuny. edu Abstract It is widely believed that the differentiation of embryonic stem cells (ESCs) into viable endothelial cells (ECs) for use in vascular tissue engineering can be enhanced by mechanical forces. In our previous work, we reported that shear stress enhanced important EC functional genes on a CD31/CD45 cell population derived from mouse ESC committed to the EC lineage. In the present study, in contrast to the effects of shear stress on this cell population, we observed that cyclic strain significantly reduced the expression of EC‐specific marker genes (vWF, VE‐cadherin, and PECAM‐1), tight junction protein genes (ZO‐1, OCLD, and CLD5), and vasoactive genes (eNOS and ET1), while it did not alter the expression of COX2. Taken together, these studies indicate that only shear stress, not cyclic strain, is a useful mechanical stimulus for enhancing the properties of CD31/CD45 cells for use as EC in vascular tissue engineering. To begin examining the mechanisms controlling cyclic strain‐ induced suppression of gene expression in CD31/CD45 cells, we depleted the heparan sulfate (HS) component of the glycocalyx, blocked integrins, and silenced the HS proteoglycan syndecan‐4 in separate experiments. All of these treatments resulted in the reversal of cyclic strain‐induced gene suppression. The current study and our previous work provide a deeper understanding of the mechanisms that balance the influence of cyclic strain and shear stress in endothelial cells.
RT-Sketch: Goal-Conditioned Imitation Learning from Hand-Drawn Sketches

Natural language and images are commonly used as goal representations in goal-conditioned imitation learning (IL). However, natural language can be ambiguous and images can be over-specified. In this work, we propose hand-drawn sketches as a modality for goal specification in visual imitation learning. Sketches are easy for users to provide on the fly like language, but similar to images they can also help a downstream policy to be spatially-aware and even go beyond images to disambiguate task-relevant from task-irrelevant objects. We present RT-Sketch, a goal-conditioned policy for manipulation that takes a hand-drawn sketch of the desired scene as input, and outputs actions. We train RT-Sketch on a dataset of paired trajectories and corresponding synthetically generated goal sketches. We evaluate this approach on six manipulation skills involving tabletop object rearrangements on an articulated countertop. Experimentally we find that RT-Sketch is able to perform on a similar level to image or language-conditioned agents in straightforward settings, while achieving greater robustness when language goals are ambiguous or visual distractors are present. Additionally, we show that RT-Sketch has the capacity to interpret and act upon sketches with varied levels of specificity, ranging from minimal line drawings to detailed, colored drawings. For supplementary material and videos, please refer to our website: http://rt-sketch.github. io.
Semantic Code Refactoring for Abstract Data Types

Modifications to the data representation of an abstract data type (ADT) can require significant semantic refactoring of the code. Motivated by this observation, this paper presents a new method to automate semantic code refactoring tasks. Our method takes as input the original ADT implementation, a new data representation, and a so-called relational representation invariant (relating the old and new data representations), and automatically generates a new ADT implementation that is semantically equivalent to the original version. Our method is based on counterexample-guided inductive synthesis (CEGIS) but leverages three key ideas that allow it to handle real-world refactoring tasks. First, our approach reduces the underlying relational synthesis problem to a set of (simpler) programming-by-example problems, one for each method in the ADT. Second, it leverages symbolic reasoning techniques, based on logical abduction, to deduce code snippets that should occur in the refactored version. Finally, it utilizes a notion of partial equivalence to make inductive synthesis much more effective in this setting. We have implemented the proposed approach in a new tool called Revamp for automatically refactoring Java classes and evaluated it on 30 Java class mined from Github. Our evaluation shows that Revamp can correctly refactor the entire ADT in 97% of the cases and that it can successfully re-implement 144 out of the 146 methods that require modifications.
On criminalized livelihoods and community forestry : a case study of traditional forest use by tribal communities in South Gujarat, India

ii PREFACE . iii TABLE OF CONTENTS . v LIST OF TABLES . viii LIST OF FIGURES . ix LIST OF ABBREVIATIONS . x ACKNOWLEDGEMENTS . xii DEDICATION . xv CHAPTER
Alterna-Moist and dry heating-induced changes in protein molecular structure, protein subfractions, and nutrient profiles in camelina seeds

The objectives of the present study were to investigate the nutritive value of camelina seeds ( Camelina sativa L. Crantz) in ruminant nutrition and to use molecular spectroscopy as a novel technique to quantify the heat-induced changes in protein molecular structures in relation to protein digestive behavior in the rumen and intestine of dairy cattle. In this study, camelina seeds were used as a model for feed protein. The seeds were kept as raw (control) or heated in an autoclave (moist heating) or in an air-draft oven (dry heating) at 120°C for 60 min. The parameters evaluated were (1) chemical profiles, (2) Cornell Net Protein and Carbohydrate System protein subfractions, (3) nutrient digestibilities and estimated energy values, (4) in situ rumen degradation and intestinal digestibility, and (5) protein molecular structures. Compared with raw seeds, moist heating markedly decreased (52.73 to 20.41%) the content of soluble protein and increased (2.00 to 9.01%) the content of neutral detergent insoluble protein in total crude protein (CP). Subsequently, the rapidly degradable Cornell Net Protein and Carbohydrate System CP fraction markedly decreased (45.06 to 16.69% CP), with a concomitant increase in the intermediately degradable (45.28 to 74.02% CP) and slowly degradable (1.13 to 8.02% CP) fractions, demonstrating a decrease in overall protein degradability in the rumen. The in situ rumen incubation study revealed that moist heating decreased (75.45 to 57.92%) rumen-degradable protein and increased (43.90 to 82.95%) intestinal digestibility of rumen-undegradable protein. The molecular spectroscopy study revealed that moist heating increased the amide I-to-amide II ratio and decreased α-helix and α-helix-to-β-sheet ratio. In contrast, dry heating did not significantly change CP solubility, rumen degrad-ability, intestinal digestibility, and protein molecular structures compared with the raw seeds. Our results indicated that, compared with dry heating, moist heating markedly changed protein chemical profiles, protein subfractions, rumen protein degradability, and intestinal digestibility, which were associated with changes in protein molecular structures (amide I-to-amid II ratio and α-helix-to-β-sheet ratio). Moist heating improved the nutritive value and utilization of protein in cam-elina seeds compared with dry heating.
Crafting minds and communities with Minecraft [version 2; peer review: 2 approved]

Minecraft is a first-person perspective video game in which players roam freely in a large three-dimensional environment. Players mine the landscape for minerals and use these minerals to create structures ( e.g. , houses) and mould the landscape. But can Minecraft be used to craft communities and minds? In this opinion piece, we highlight the enormous potential of Minecraft for fostering social connectedness, collaboration
Sev-Pregnancy per artificial insemination in lactating dairy cows subjected to 2 different intervals from presynchronization to initiation of Ovsynch protocol

A protocol for presynchronization of ovarian status with 2 injections of PGF 2α given 14 d apart, with the last PGF 2α injection given 12 or 14 d before Ovsynch increases pregnancy per artificial insemination (P/AI) in dairy cows. We determined the efficacy of reducing the interval from the last PGF 2α injection (500 μg of cloprostenol) of presynchronization to initiation of Ovsynch on response to treatment and P/AI. Lactating dairy cows were assigned to an Ovsynch protocol, with the initial injection of GnRH given either 9 (PRE-9; n = 135) or 12 d (PRE-12; n = 135) after the second PGF 2α injection of presynchronization. The Ovsynch protocol consisted of 2 injections of 100 μg of GnRH given 9 d apart and 1 injection of PGF 2α given 7 d after the initial GnRH injection, and cows were subjected to timed artificial insemination (TAI; 70 ± 3.5 DIM) approximately 16 h after the second GnRH injection. Body condition score (1–5 scale) was recorded at TAI. Blood samples were taken for progesterone determination at the PGF 2α injection of Ovsynch, at TAI, and at 11 d after TAI. Ultrasonographic examinations were done in all cows at the second PGF 2α injection of presynchronization, initial GnRH injection, PGF 2α injection of Ovsynch, at TAI, and 24 h after TAI for cy-clicity status and ovarian responses to treatments, and at 32 and 60 d after TAI for confirmation of pregnancy. Overall, 29 cows (10.7%) were determined acyclic or cystic and excluded from the study. The percentage of cows responding to initial GnRH injection (62.2 vs. 61.5%) did not differ between PRE-9 and PRE-12 but more cows in the PRE-9 group failed to respond to PGF 2α treatment of Ovsynch compared with PRE-12 (22.7 vs. 10.7%). Body condition score at TAI (2.9 ± 0.02) and mean ovulatory follicle diameter (16.4 ± 0.2 mm) were not different between treatments. Overall P/ AI at 32 d was reduced in PRE-9 (33.6%) compared with PRE-12 (44.3%) but pregnancy losses (5.0 vs. 3.7%) did not differ between treatments. Primiparous cows in the PRE-12 group had higher mean progesterone concentration 11 d after TAI and greater P/AI 32 after TAI than primiparous cows in the PRE-9 group (6.4 ± 0.5 vs. 4.6 ± 0.5 ng/mL and 55.8 vs. 30.0%, respectively). In conclusion, reducing the interval from the last PGF 2α injection of the presynchronization treatment to initiation of Ovsynch (from 12 to 9 d) did not affect ovulatory response to initial GnRH injection but reduced response to PGF 2α injection of Ovsynch and P/AI at 32 and 60 d after TAI. The reduction in P/AI was particularly evident in primiparous cows of the PRE-9 group.
Understanding Neural ODEs prediction decision using SHAP

Neural ordinary differential equations (NODEs) have emerged as a powerful approach for modelling complex dynamic systems using continuous-time transformations. Although NODEs offer superior modelling capabilities, little research has been conducted on understanding the factors that contribute to their predictions on image datasets. In this paper, we propose the leveraging of SHapley Additive exPlanations (SHAP), which is an influential explainable artificial intelligence method, to gain insights into the NODEs prediction process. We enable the interpretable analysis of important pixels that contribute to the prediction decisions of NODEs by adapting SHAP to the continuous-time nature thereof. Experiments on synthetic datasets demonstrate the efficacy of our proposed approach in revealing the dynamics and important features that drive NODEs predictions. Our empirical findings provide insights into how NODEs determine important features and the distributions of the Shapley values of each class. The proposed integration of SHAP with NODEs contributes to the broader goal of enhancing transparency and trustworthiness in the application of continuous-time models to complex real-world systems.
strate-Invited review: Determinants of farmers’ adoption of management-based strategies for infectious disease prevention and control

The prevention and control of endemic pathogens within and between farms often depends on the adoption of best management practices. However, farmers regularly do not adopt recommended measures or do not enroll in voluntary disease control programs. This indicates that a more comprehensive understanding of the influences and extension tools that affect farmers’ management decisions is necessary. Based on a review of relevant published literature, we developed recommendations to support policy-makers, industry representatives, researchers, veterinarians, and other stakeholders when motivating farmers to adopt best management practices, and to facilitate the development and implementation of voluntary prevention and control programs for livestock diseases. Farmers will make management decisions based on their unique circumstances, agricultural contexts, beliefs, and goals. Providing them with rational but universal arguments might not always be sufficient to motivate on-farm change. Implementation of recommended management practices is more likely if farmers acknowledge the existence of a problem and their responsibility to take action. The perceived feasibility and effectiveness of the recommended management strategy and sufficient technical knowledge further increase the likelihood of adequate adoption. Farmers will also weigh the expected advantages of a proposed change against the expected disadvantages, and these considerations often include internal drivers such as pride or the desire to conform with perceived standards. Extension tools and farmers’ social referents (e.g., veterinarians, peers) not only provide technical information but also influence these standards. Whereas mass media have the potential to deliver information to a broad audience, more personal approaches such as participatory group learning or individual communication with farm advisors can enable the tailoring of recommendations to farmers’ situations. Approaches that appeal to farmers’ internal motivators or that unconsciously elicit the desired behavior will increase the success of the intervention. Collaboration among stakeholders, assisted by social scientists and communication specialists, is necessary to provide a context that facilitates on-farm change and transfers consistent messages across extension tools in the most effective way.
Depressive symptoms in caregivers of patients with dementia: demographic variables and burden

Objective: Individuals suffering from dementia are affected by a progressive and significant global deterioration and, consequently, might require longer assistance in the advanced stage of the illness. The illness is a great burden on the person who takes care of a patient, namely, the caregiver. This study aims to analyze the presence and relationship of specific sociodemographic variables, subjective burden, and depressive symptoms among caregivers of patients with dementia. Methods: The participants of this study were caregivers at a health care unit for the elderly in southern Italy. An evaluation of the burden of patients with dementia on caregivers was carried out using the Caregiver Burden Inventory (CBI) and depressive symptoms using the Self-Rating Depression Scale (SDS). Results: A total of 150 caregivers completed the study. In all, 83 (55%) caregivers showed a total CBI score $ 36, of whom 70% showed pathological depression scores in SDS. According to SDS, 28 (19%) caregivers showed a total CBI score from 24 to 36, of whom 32% were depressed. Depression was present in 5% of the caregivers whose CBI score was , 24. Hence, an association between burden and depression was evident ( χ 2 = 47.446, P , 0.001). A multiple linear regression analysis showed that depression (adjusted R 2 = 0.622, F = 50.123, P , 0.001) was associated with higher physical ( β = 0.666, P = 0.001) and developmental ( β = 0.712, P , 0.001) burdens, lower socioeconomic status ( β =- 4.282; P = 0.002), higher level of urbanicity ( β = 3.070; P = 0.012), and advanced age ( β = 2.132; P = 0.08). Conclusion: Our study confirms the presence of depressive symptoms in a large number of caregivers with high burden. Nevertheless, this study demonstrates that depressive symptoms are mainly associated with sociodemographic variables and, to a lesser degree, physical and developmental burdens.
Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy

The prevalence and burden of autoimmune and autoantibody mediated disease is increasing worldwide, yet most disease etiologies remain unclear. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leverage advances in programmable-phage immunoprecipitation (PhIP-Seq) methodology to explore the modulation, or lack thereof, of proteome-wide autoantibody profiles in both health and disease. We demonstrate that each individual, regardless of disease state, possesses a distinct set of autoreactivities constituting a unique immunological fingerprint, or autoreactome, that is remarkably stable over years. In addition to uncovering important new biology, the autoreactome can be used to better evaluate the relative effectiveness of various therapies in altering autoantibody repertoires. We find that therapies targeting B-Cell Maturation Antigen (BCMA) profoundly alter an individuals autoreactome, while anti-CD19 and CD-20 therapies have minimal effects, strongly suggesting a rationale for BCMA or other plasma cell targeted therapies in autoantibody mediated diseases.
Safety and efficacy of dinutuximab in the treatment of neuroblastoma: A review

Dinutuximab, which is a monoclonal antibody targeting GD2 expressed in neuroblasts, improves survival when included in the therapy regimen. This article reviews the importance of dinutuximab in managing neuroblastoma (NB). Dinutuximab targets high levels of GD2 expression in NB cells, thus increasing event-free survival when used in the maintenance therapy of high-risk patients with NB. Although several collaborative studies have set the standard of care for maintenance therapy, the long-term follow-up and continuous evaluation of the use of antibodies and the co-administration of other pharmacological or immunomodulatory drugs remain to be studied. Trials have shown that the use of dinutuximab for maintenance therapy can prolong the time before the first relapse and improve overall survival. However, there is uncertainty in the function of cytokines co-administered with dinutuximab, which may lead to increased toxicity without additional benefits. Recent studies on relapsed and refractory NB have shown the potential efficacy of dinutuximab. Further research is required to properly incorporate Dinutuximab in current treatment modalities.