Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Feedstock Variability, Feedstock Blends, and Pretreatment Conditions on Sugar Yield and Production Costs

Mass production of sustainable biofuels replacing fossil fuels will significantly reduce global greenhouse gas emissions. However, biomass feedstock variability, availability, and affordability pose significant risks for the sustainable production of biofuels in biorefinery plants. To derisk the sustainable production of biofuels, this work investigates the sugar yields and production costs of four different feedstocks as well as their blends, using different pretreatment methods: deacetylation and dilute acid pretreatment (DDA) and deacetylation and mechanical refining pretreatment (DMR). We found that not only feedstock species variability, but also feedstock harvesting techniques have large impacts on both sugar yields and production costs. Single-pass harvested corn stover (SPCS) showed higher sugar yields and lower production costs than multipass harvested corn stover, followed by sorghum and switchgrass. The highest glucose yields of 91% and 95.3%, which corresponds to the lowest sugar production costs of $0.2286/lb. and $0.2490/lb. , were observed for SPCS using DDA and DMR, respectively. The difference in sugar yields and production costs due to feedstock variability can be largely mitigated by increasing deacetylation severity, especially in DMR. Higher deacetylation severity resulted in decreased sugar production costs in the case of DMR in contrast to increased costs in the case of DDA. Blending switchgrass and sorghum into corn stover, which can significantly increase the feedstock availability and sustainability, resulted in sugar yields and production costs of roughly the weighted average of those derived from constituent individual feedstocks, respectively. Thus, blending feedstocks of different biomass species is a potential successful strategy for sustainable production of biofuels to replace fossil-derived fuels.
Pretherapeutic Assessment of Pancreatic Cancer: Comparison of FDG PET/CT Plus Delayed PET/MR and Contrast-Enhanced CT/MR

Purpose This study aims to determine the diagnostic performance of whole-body FDG PET/CT plus delayed abdomen PET/MR imaging in the pretherapeutic assessment of pancreatic cancer in comparison with that of contrast-enhanced (CE)-CT/MR imaging. Materials and Methods Forty patients with pancreatic cancer underwent nonenhanced whole-body FDG PET/CT, delayed abdomen PET/MR imaging, and CE-CT/MR imaging. Two nuclear medicine physicians independently reviewed these images and discussed to reach a consensus, determining tumor resectability according to a 5-point scale, N stage (N0 or N positive), and M stage (M0 or M1). With use of clinical-surgical-pathologic findings as the reference standard, diagnostic performances of the two imaging sets were compared by using the McNemar test. Results The diagnostic performance of FDG PET/CT plus delayed PET/MR imaging was not significantly different from that of CE-CT/MR imaging in the assessment of tumor resectability [area under the receiver operating characteristic curve: 0.927 vs. 0.925 (p = 0.975)], N stage (accuracy: 80% (16 of 20 patients) vs. 55% (11 of 20 patients), p = 0.125), and M stage (accuracy: 100% (40 of 40 patients) vs. 93% (37 of 40 patients), p = 0.250). Moreover, 14 of 40 patients had liver metastases. The number of liver metastases detected by CE-CT/MR imaging, PET/CT, and PET/MR imaging were 33, 18, and 61, respectively. Compared with CE-CT/MR imaging, PET/MR imaging resulted in additional findings of more liver metastases in 9/14 patients, of which 3 patients were upstaged. Compared with PET/CT, PET/MR imaging resulted in additional findings of more liver metastases in 12/14 patients, of which 6 patients were upstaged. Conclusions Although FDG PET/CT plus delayed PET/MR imaging showed a diagnostic performance similar to that of CE-CT/MR imaging in the pretherapeutic assessment of the resectability and staging of pancreatic tumors, it still has potential as the more efficient and reasonable work-up approach for the additional value of metastatic information provided by delayed PET/MR imaging.
Genetic Determinants of Serum Calcification Propensity and Cardiovascular Outcomes in the General Population

Background: Serum calciprotein particle maturation time (T50), a measure of vascular calcification propensity, is associated with cardiovascular morbidity and mortality. We aimed to identify genetic loci associated with serum T50 and study their association with cardiovascular disease and mortality. Methods: We performed a genome-wide association study of serum T50 in 2,739 individuals of European descent participating in the Prevention of REnal and Vascular ENd-stage Disease (PREVEND) study, followed by a two-sample Mendelian randomization (MR) study to examine causal effects of T50 on cardiovascular outcomes. Finally, we examined associations between T50 loci and cardiovascular outcomes in 8,566 community-dwelling participants in the Rotterdam study. Results: We identified three independent genome-wide significant single nucleotide polymorphism (SNPs) in the AHSG gene encoding fetuin-A: rs4917 (p = 1.72 × 10−101), rs2077119 (p = 3.34 × 10−18), and rs9870756 (p = 3.10 × 10−8), together explaining 18.3% of variation in serum T50. MR did not demonstrate a causal effect of T50 on cardiovascular outcomes in the general population. Patient-level analyses revealed that the minor allele of rs9870756, which explained 9.1% of variation in T50, was associated with a primary composite endpoint of all-cause mortality or cardiovascular disease [odds ratio (95% CI) 1.14 (1.01–1.28)] and all-cause mortality alone [1.14 (1.00–1.31)]. The other variants were not associated with clinical outcomes. In patients with type 2 diabetes or chronic kidney disease, the association between rs9870756 and the primary composite endpoint was stronger [OR 1.40 (1.06–1.84), relative excess risk due to interaction 0.54 (0.01–1.08)]. Conclusions: We identified three SNPs in the AHSG gene that explained 18.3% of variability in serum T50 levels. Only one SNP was associated with cardiovascular outcomes, particularly in individuals with type 2 diabetes or chronic kidney disease.
MicroRNA-92a-3p Enhances Cisplatin Resistance by Regulating Krüppel-Like Factor 4-Mediated Cell Apoptosis and Epithelial-to-Mesenchymal Transition in Cervical Cancer

Recent studies have confirmed the existence and key roles of microRNA (miRNAs) in cancer drug resistance, including cervical cancer (CC). The present study aims to establish a novel role for miR-92a-3p and its associated gene networks in cisplatin (DDP) resistance of CC. First, the disparities in miRNA expression between CC tissues and adjacent normal tissues were screened based on GSE19611 microarray data that retrieved from Gene Expression Omnibus (GEO), and we identified several miRs that were significantly downregulated or upregulated in CC tissues including miR-92a-3p. Moreover, miR-92a-3p was significantly up-regulated in DDP-resistant cells and was the most differently expressed miRNA. Functionally, knockdown of miR-92a-3p increased the sensitivity of DDP-resistant cells to DDP via inhibiting cell proliferation, migration and invasion, and promoting apoptosis. Conversely, overexpression of miR-92a-3p significantly induced DDP resistance in CC parental cells including HeLa and SiHa cells. Moreover, Krüppel-like factor 4 (KLF4) was identified as a direct target of miR-92a-3p, and an obvious inverse correlation was observed between the expression of miR-92a-3p and KLF4 in 40 pairs of cancer tissues. Furthermore, KLF4 knockdown reversed the promoting effect of miR-92a-3p inhibition on DDP sensitivity in DDP-resistant CC cells. Besides, high expression of miR-92a-3p was associated with DDP resistance, as well as a short overall survival in clinic. Taken together, these findings provide important evidence that miR-92a-3p targets KLF4 and is significant in DDP resistance in CC, indicating that miR-92a-3p may be an attractive target to increase DDP sensitivity in clinical CC treatment.
Relationship Between the Pyroptosis Pathway and Epilepsy: A Bioinformatic Analysis

Purpose This study aimed to analyse the correlation between the pyroptosis pathway and epilepsy using bioinformatics analysis technology. We analyzed the expression of gasdermin D (GSDMD) and gasdermin E (GSDME), the key molecules of pyroptosis, in kainic acid-induced epileptic mice. Methods Weighted gene co-expression network analysis (WGCNA) was used to construct a signed co-expression network from expression data to screen gene sets closely related to epilepsy. The correlation between the module and epilepsy was verified through module conservative analysis, gene ontology (GO) annotation analysis, and correlation analysis with known epilepsy genes. We obtained currently recognized pyroptosis-related molecules through literature review, and correlation analysis was used to evaluate their correlation with epilepsy. Differentially expressed gene (DEG) analysis was used to analyse expression changes of pyroptosis-related molecules at the transcriptome level, compared to the sham group. We subsequently established a kainic acid-induced status epilepticus (SE) model in mice and validated the mRNA and protein expression of GSDMD and GSDME, the key molecules of pyroptosis, by quantitative reverse transcription PCR (qRT-PCR) and western blotting (WB). Results Using WGCNA, module conservative analysis, and correlation analysis with known epilepsy genes, we screened out a module (a gene set of interest) closely related to epilepsy that was prominently enriched in immune and inflammatory-related biological processes. Correlation analysis results suggest that pyroptosis-related molecules are closely related to this module, but have no obvious correlation with others. DEG analysis of molecules associated with pyroptosis suggests that most of the pyroptosis-related molecules had significantly increased expression after SE, such as IL1b, Casp1, Casp4, Pycard, Gsdmd, Nlrp3, Aim2, Mefv, Tlr2, Tlr3, and Tlr4. qRT-PCR and WB analysis confirmed that the mRNA and protein levels of GSDMD in the mouse hippocampus were significantly upregulated after SE. The mRNA expression of GSDME was not different between the epilepsy group and sham group. However, the WB results showed that the expression of full-length GSDME was decreased and GSDME-N-terminus were significantly increased after SE. Conclusions Our study highlights that the pyroptosis pathway may be closely related to epilepsy. GSDMD and GSDME, the key executive molecules of pyroptosis, will help to understand the pathogenesis of epilepsy and aid in discovering new targets for anti-epileptic drug treatments.
HIV-1–Specific Immunodominant T-Cell Responses Drive the Dynamics of HIV-1 Recombination Following Superinfection

A series of HIV-1 CRF01_AE/CRF07_BC recombinants were previously found to have emerged gradually in a superinfected patient (patient LNA819). However, the extent to which T-cell responses influenced the development of these recombinants after superinfection is unclear. In this study, we undertook a recombination structure analysis of the gag, pol, and nef genes from longitudinal samples of patient LNA819. A total of 9 pol and 5 nef CRF01_AE/CRF07_BC recombinants were detected. The quasispecies makeup and the composition of the pol and nef gene recombinants changed continuously, suggestive of continuous evolution in vivo. T-cell responses targeting peptides of the primary strain and the recombination regions were screened. The results showed that Pol-LY10, Pol-RY9, and Nef-GL9 were the immunodominant epitopes. Pol-LY10 overlapped with the recombination breakpoints in multiple recombinants. For the LY10 epitope, escape from T-cell responses was mediated by both recombination with a CRF07_BC insertion carrying the T467E/T472V variants and T467N/T472V mutations originating in the CRF01_AE strain. In pol recombinants R8 and R9, the recombination breakpoints were located ~23 amino acids upstream of the RY9 epitope. The appearance of new recombination breakpoints harboring a CRF07_BC insertion carrying a R984K variant was associated with escape from RY9-specific T-cell responses. Although the Nef-GL9 epitope was located either within or 10~11 amino acids downstream of the recombination breakpoints, no variant of this epitope was observed in the nef recombinants. Instead, a F85V mutation originating in the CRF01_AE strain was the main immune escape mechanism. Understanding the cellular immune pressure on recombination is critical for monitoring the new circulating recombinant forms of HIV and designing epitope-based vaccines. Vaccines targeting antigens that are less likely to escape immune pressure by recombination and/or mutation are likely to be of benefit to patients with HIV-1.
Cryptanalysis of the Cryptosystems Based on the Generalized Hidden Discrete Logarithm Problem

The hidden discrete logarithm problem(HDLP) over non-commutative associative algebras (FNAAs) in [1] was broken in [8] by reducing to discrete logarithm problem(DLP) in a ﬁnite ﬁeld through analyzing the eigenvalues of the representation matrix. A generalized form of HDLP(GHDLP) was proposed in [11], which is claimed to be computationally hard under quantum computers. Based on this, several schemes are proposed. In this paper, we will show that GHDLP can also be reduced to DLP in a ﬁnite ﬁeld by algebraic representation. With all the instruments in hand, we will show how some schemes based on GHDLP can be broken. Thus we conclude that these schemes are not secure under quantum attack. So constructing schemes based on GHDLP is fundamentally wrong.
The Effect of Digital Citizenship on Negative Online Behaviors and Learning Outcomes in Higher Education

With the increase in Internet use, there has been an upsurge in negative online behaviors (such as cyberbullying and online harassment) among college students. As a result of the negative online behaviors, many students may experience anxiety, depression, feelings of loneliness, and alienation, which ultimately can impact their well-being and interfere with their ability to learn. It is envisaged that extending digital citizenship behavior to educational settings will arrest, or at the very least help mitigate, the impact of these negative behaviors on student learning outcomes. Using data collected from 184 university students, results show that perceived learning outcomes indirectly impact the relationship between digital citizenship and cyberbullying behaviors.
PACE: Fully Parallelizable BFT from Reproposable Byzantine Agreement

The classic asynchronous Byzantine fault tolerance (BFT) framework of Ben-Or, Kemler, and Rabin (BKR) and its descendants rely on reliable broadcast (RBC) and asynchronous binary agreement (ABA). However, BKR does not allow all ABA instances to run in parallel, a well-known performance bottleneck. We propose PACE, a generic framework that removes the bottleneck, allowing fully parallelizable ABA instances. PACE is built on RBC and reproposable ABA (RABA). Different from the conventional ABA, RABA allows a replica to change its mind and vote twice. We show how to efficiently build RABA protocols from existing ABA protocols and a new ABA protocol that we introduce. We implement six new BFT protocols: three in the BKR framework, and three in the PACE framework. Via a deployment using 91 replicas on Amazon EC2 across five continents, we show that all PACE instantiations, in both failure-free and failure scenarios, significantly outperform their BKR counterparts, and prior BFT protocols such as BEAT and Dumbo, in terms of latency, throughput, latency vs. throughput, and scalability.
In vitro Inoculation of Fresh or Frozen Rumen Fluid Distinguishes Contrasting Microbial Communities and Fermentation Induced by Increasing Forage to Concentrate Ratio

In vitro rumen batch culture is a technology to simulate rumen fermentation by inoculating microorganisms from rumen fluids. Although inocula (INO) are commonly derived from fresh rumen fluids, frozen rumen fluids are also employed for the advantages of storing, transporting, and preserving rumen microorganisms. The effects of frozen INO on microbial fermentation and community may be interfered with by substrate type, which has not been reported. This study was designed to test whether rumen fluid treatments (i.e., fresh and frozen) could interact with incubated substrates. A complete block design with fractional arrangement treatment was used to investigate the effects of INO (fresh or frozen rumen fluids) and concentrate-to-forage ratios (C/F, 1:4 or 1:1) on rumen fermentation and microbial community. The effects of increasing C/F were typical, including increased dry matter (DM) degradation and total volatile fatty acids (VFA) concentration (P < 0.001), and decreased acetate to propionate ratio (P = 0.01) and bacterial diversity of richness and evenness (P ≤ 0.005) with especially higher fermentative bacteria such as genus Rikenellaceae_RC, F082, Prevotella, Bacteroidales_BS11, Muribaculaceaege, and Christensenellaceae_R-7 (P ≤ 0.04). Although frozen INO decreased (P < 0.001) DM degradation and altered rumen fermentation with lower (P ≤ 0.01) acetate to propionate ratio and molar proportion of butyrate than fresh INO, typical effects of C/F were independent of INO, as indicated by insignificant INO × C/F interaction on substrate degradation, VFA profile and bacterial community (P ≥ 0.20). In summary, the effect of C/F on fermentation and bacterial diversity is not interfered with by INO type, and frozen INO can be used to distinguish the effect of starch content.
Threats to Neglected Biodiversity: Conservation Success Requires More Than Charisma

Our planet is home to an incredible array of species; however, relatively few studies have compared how anthropogenic threats impact taxonomic groups over time. Our objective was to identify temporal trends in threats facing the four most speciose phyla protected by the United States Endangered Species Act: angiosperms, arthropods, chordates, and mollusks. We determined presence or absence of threats for each species in these phyla by reviewing Final Rule listing decisions. For each phylum, we evaluated whether there was a linear, quadratic, or pseudo-threshold association between year of listing and the presence of 24 anthropogenic threats. We identified temporal trends for 80% of the 96 threat-phylum combinations. We classified threats as topmost (probability of being included in a species' listing decision peaking at ≥ 0.81) and escalating (probability of being included in a listing decision increasing by ≥ 0.81 between a species' first and most recent years of listing). Angiosperms, arthropods, and mollusks each had more topmost and escalating threats than chordates. Percentages of topmost threats were 42.9% (N = 21) for mollusks, 36.4% (N = 22) for angiosperms, and 33.3% (N = 21) for arthropods. Percentages of escalating threats were 22.7% (N = 22) for angiosperms and 14.3% (N = 21) for arthropods and mollusks. In contrast, percentages of topmost and escalating threats were only 4.2% (N = 24) for chordates, this one threat being climate change. Our research suggests potential conservation successes; some overutilization and pollution threats showed only gradually increasing or declining trends for certain phyla. We identified authorized take impacting angiosperms as the sole threat-phylum combination for which the threat had been consistently decreasing since the phylum's first year of listing. Conversely, species interactions, environmental stochasticity, and demographic stochasticity threats have seen drastic increases across all phyla; we suggest conservation efforts focus on these areas of increasing concern. We also recommend that resources be allocated to phyla with numerous topmost and escalating threats, not just to chordates.
Occluded and tiny face detection network for dense crowd

Face detection, which palys a crucial part in face related applications, has been widely developed in the past decades. However, detecting occluded and tiny faces still remains great challenges due to two inherent problems: the excessive number of redundant smaples, and few effective features for detection. Most previous approachs cannot essentially filter out the redundant samples and fail to take full advantage of existing effective features. Therefore, the detection accuracy of occluded face and tiny face cannot be improved simultaneously. To overcome these problems, we put forward a occluded and tiny face detection network (OTFD), aiming to enhance the ability of detecting occluded and tiny faces simultaneously especially in dense crowd. OTFD consists of filter subnet, connection subnet and precise subnet in a parallel structure. Among them, the filter subnet is used to delete the excessive redundant samples and reduce the complexity of training process. The connection subnet is designed to achieve the fusion of features from shallow and deep layers, and the semantic information from deep layers are supplemented to shallow layers. In precise subnet, the anchors and features have been filtered and enriched in filter and connection subnets, which is helpful to make precise classification and regression in this subnet. Furthermore, in order to solve the problem of few effective features for detection, in filter subnet, we propose the feature compensation module (FCM) to reduce the inevitable feature loss caused by convolution operation, which makes the most of existing features in occluded and tiny faces. Last but not least, with the purpose of improving the anti-interference ability of detector in dense crowd, a repulsive loss function is presented to enhance the robustness of detector in complex backgrounds. Extensive experiments are conducted on wider face dataset, and our method achieves superior performance compared with other corresponding methods.
Hecate: Abuse Reporting in Secure Messengers with Sealed Sender

End-to-end encryption provides strong privacy protections to billions of people, but it also compli-cates efforts to moderate content that can seriously harm people. To address this concern, Tyagi et al. [CRYPTO 2019] introduced the concept of asymmetric message franking (AMF) so that people can report abusive content to a moderator, while otherwise retaining end-to-end privacy by default and compatibility with anonymous communication systems like Signal’s sealed sender. In this work, we provide a new construction for asymmetric message franking called Hecate that is faster, more secure, and introduces additional functionality compared to Tyagi et al. First, our construction uses fewer invocations of standardized crypto primitives and operates in the plain model. Second, on top of AMF’s accountability and deniability requirements, we also add forward and backward secrecy. Third, we combine AMF with source tracing, another approach to content moderation that has previously been considered only in the setting of non-anonymous networks. Source tracing allows for messages to be forwarded, and a report only identifies the original source who created a message. To provide anonymity for senders and forwarders, we introduce a model of AMF with preprocessing whereby every client authenticates with the moderator out-of-band to receive a token that they later consume when sending a message anonymously.
Rule-based Languages for Reasoning on Data : Analysis, Design and Applications

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Rule-based Languages for Reasoning on Data : Analysis, Design and Applications Federico Ulliana