Miracle-dz/UniFAR-FTUs huggingface dataset:
A Survey on Societal Event Forecasting with Deep Learning

Population-level societal events, such as civil unrest and crime, often have a significant impact on our daily life. Forecasting such events is of great importance for decision-making and resource allocation. Event prediction has traditionally been challenging due to the lack of knowledge regarding the true causes and underlying mechanisms of event occurrence. In recent years, research on event forecasting has made significant progress due to two main reasons: (1) the development of machine learning and deep learning algorithms and (2) the accessibility of public data such as social media, news sources, blogs, economic indicators, and other meta-data sources. The explosive growth of data and the remarkable advancement in software/hardware technologies have led to applications of deep learning techniques in societal event studies. This paper is dedicated to providing a systematic and comprehensive overview of deep learning technologies for societal event predictions. We focus on two domains of societal events: \textit{civil unrest} and \textit{crime}. We first introduce how event forecasting problems are formulated as a machine learning prediction task. Then, we summarize data resources, traditional methods, and recent development of deep learning models for these problems. Finally, we discuss the challenges in societal event forecasting and put forward some promising directions for future research.
Depletion of Cyclophilins B and C Leads to Dysregulation of Endoplasmic Reticulum Redox Homeostasis*

Background: Cyclophilins catalyze cis-trans isomerization of peptidyl-prolyl bonds. Results: Depletion of cyclophilins B and C results in endoplasmic reticulum (ER) hyperoxidation including more oxidized protein-disulfide isomerase enzymes and elevated oxidized:total glutathione ratio. Conclusion: Cyclophilins B and C participate in ER redox homeostasis. Significance: An unexpected level of ER redox regulation is revealed that likely contributes to cyclosporine A-induced oxidative stress. Protein folding within the endoplasmic reticulum is assisted by molecular chaperones and folding catalysts that include members of the protein-disulfide isomerase and peptidyl-prolyl isomerase families. In this report, we examined the contributions of the cyclophilin subset of peptidyl-prolyl isomerases to protein folding and identified cyclophilin C as an endoplasmic reticulum (ER) cyclophilin in addition to cyclophilin B. Using albumin and transferrin as models of cis-proline-containing proteins in human hepatoma cells, we found that combined knockdown of cyclophilins B and C delayed transferrin secretion but surprisingly resulted in more efficient oxidative folding and secretion of albumin. Examination of the oxidation status of ER protein-disulfide isomerase family members revealed a shift to a more oxidized state. This was accompanied by a >5-fold elevation in the ratio of oxidized to total glutathione. This “hyperoxidation” phenotype could be duplicated by incubating cells with the cyclophilin inhibitor cyclosporine A, a treatment that triggered efficient ER depletion of cyclophilins B and C by inducing their secretion to the medium. To identify the pathway responsible for ER hyperoxidation, we individually depleted several enzymes that are known or suspected to deliver oxidizing equivalents to the ER: Ero1αβ, VKOR, PRDX4, or QSOX1. Remarkably, none of these enzymes contributed to the elevated oxidized to total glutathione ratio induced by cyclosporine A treatment. These findings establish cyclophilin C as an ER cyclophilin, demonstrate the novel involvement of cyclophilins B and C in ER redox homeostasis, and suggest the existence of an additional ER oxidative pathway that is modulated by ER cyclophilins.
Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs)

Matrix metalloproteinases (MMPs) play a critical role in physiological processes and pathological conditions such tumor invasion and metastasis. In recent years, a number of MMP inhibitors have been proposed, including the chemically modified tetracyclines (CMTs), which have been evaluated in preclinical cancer models showing promising results. This work provides insights into the structure and dynamics of the MMP-2 catalytic domain complexed with seven CMT (CMT-n), based on the analysis of molecular dynamics trajectories in solution. The comparative analysis of various relevant molecular aspects of the different complexes of MMP-2 and CMT-n derivatives was performed aiming to elucidate the effect of ligands on the enzyme structure. These include the radial distribution function of the water molecules around the catalytic zinc, the solvent accessible surface area for the inhibitors and the root-mean-square fluctuation for all amino acid residues. The results help to understand the differences in the binding modes of related compounds and, therefore, add to further design of novel tetracycline-based inhibitors for MMP enzymes.
Temporal genetic stability and high effective population size despite fisheries‐induced life‐history trait evolution in the North Sea sole

Heavy fishing and other anthropogenic influences can have profound impact on a species’ resilience to harvesting. Besides the decrease in the census and effective population size, strong declines in mature adults and recruiting individuals may lead to almost irreversible genetic changes in life‐history traits. Here, we investigated the evolution of genetic diversity and effective population size in the heavily exploited sole (Solea solea), through the analysis of historical DNA from a collection of 1379 sole otoliths dating back from 1957. Despite documented shifts in life‐history traits, neutral genetic diversity inferred from 11 microsatellite markers showed a remarkable stability over a period of 50 years of heavy fishing. Using simulations and corrections for fisheries induced demographic variation, both single‐sample estimates and temporal estimates of effective population size (Ne) were always higher than 1000, suggesting that despite the severe census size decrease over a 50‐year period of harvesting, genetic drift is probably not strong enough to significantly decrease the neutral diversity of this species in the North Sea. However, the inferred ratio of effective population size to the census size (Ne/Nc) appears very small (10−5), suggesting that overall only a low proportion of adults contribute to the next generation. The high Ne level together with the low Ne/Nc ratio is probably caused by a combination of an equalized reproductive output of younger cohorts, a decrease in generation time and a large variance in reproductive success typical for marine species. Because strong evolutionary changes in age and size at first maturation have been observed for sole, changes in adaptive genetic variation should be further monitored to detect the evolutionary consequences of human‐induced selection.
Electro-rheological description of liquid and solid dielectrics applied to two-phase polymers: a study of EPDM

A novel electro-rheological model for liquid and solid dielectrics is presented, which is well adapted to the purposes of engineering calculations. The study is focused in the frequency range of relaxation processes, well below the optical range. In addition, the dielectric material is considered to have only polarization charges, i.e. conduction charges are absent. The description for the energy transfer processes in dielectric materials is based on one-dimensional approximation using a rheological model with two- and three- parameter Voigt elements. The mean field approximation is adopted, considered as an averaging of the mechanical and electrical properties for the dipole and inter-dipole spaces. The continuity condition for mechanical and electrical forces is also taken into account. The model was applied to the study of ethylene-propylenedyene monomer (EPDM) commercial rubber having two phases, amorphous and semi-crystalline. A good agreement was found with the experimental results from dielectric relaxation and dynamical mechanical measurements
Association between plasma phosphorus and renal outcome: A prospective cohort of patients majorly with glomerulonephritis

Studies investigating the association between blood phosphorus and renal outcomes yielded inconsistent results, and studies from Asian population are extremely limited. We initiated the present cohort study, aiming to prospectively examine the association between blood phosphorus and adverse renal outcomes in a prospective chronic kidney disease (CKD) cohort of Chinese patients majorly with glomerulonephritis.
CCR5, RANTES and SDF‐1 polymorphisms and mother‐to‐child HIV‐1 transmission

Among 288 HIV‐1‐infected, breastfeeding women who received zidovudine prophylaxis and were followed with their infants in Nairobi, we found no associations between maternal genetic polymorphisms in CCR5 (59029G/A, 59353T/C, 59356T/C, 59402G/A), RANTES (‐403G/A) and SDF‐1 (3’801G/A) and mother‐to‐child HIV‐1 transmission; plasma, cervical and breastmilk viral loads; or breastmilk chemokine concentrations.
The highly conserved domain of the Caulobacter McpA chemoreceptor is required for its polar localization

We have fused GFP to the C‐terminus of McpA to study chemoreceptor polar localization in Caulobacter crescentus. The full‐length McpA–GFP fusion is polarly localized and methylated. The methylation is dependent on the chemoreceptor methyltransferase (cheR) and chemoreceptor methylesterase (cheB) genes present in the mcpA operon. C‐terminal and internal deletions of McpA were constructed and fused to the N‐terminus of GFP to identify the domains required for polar localization. When the R1 methylation domain was deleted, the McpA–GFP fusion was still polarly localized, suggesting that this domain is dispensable for polar localization. However, when the highly conserved domain (HCD), which is involved in interacting with CheW, was deleted either by an internal deletion or C‐terminal deletion, the resulting McpA–GFP fusions were completely delocalized. When the mcpA operon, which contains the cheW and cheA homologues, was deleted, the full‐length McpA–GFP fusion was delocalized. Although additional chemotaxis genes are required for the polar localization of McpA–GFP, the presence of the single polar flagellum is not required. However, in filamentous cells, which are frequently found in C. crescentus fliF mutants, the McpA–GFP fusion was observed at mid‐cell positions.
Molecular detection of bacteria in calcium carbonate powder used in cosmetic formulations

Given that a variety of bacterial species may occur in the calcium carbonate powder used for cosmetic formulations, an understanding of their diversity and abundance is necessary to accurately assess the contamination of the finished product. 16S rRNA was PCR‐amplified from genomic DNA extracted from three different calcium carbonate powder grades, and these amplicon libraries were sequenced using deep amplicon sequencing technology. The resulting libraries contained 4149–6688 16S rRNA reads per sample with a length of 327–342 bp. Classification into genus of pyrosequencing reads of the dominant bacterial species found in calcium carbonate powders was used to confirm the absence of Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella spp. and Escherichia coli. The analysis described here can be used to determine the microbial diversity of calcium carbonate powder or the presence of any ‘indicator microorganisms’ in raw materials as well as in cosmetic products. This work provides guidance for prioritizing subsequent culturable and quantitative analysis, ensuring that potentially significant microorganisms are not left out of risk estimations.
The Incidence of Complications Associated With Molding Helmet Therapy: An Avoidable Risk in the Treatment of Positional Head Deformities?

AbstractMolding helmet therapy using an individual head orthosis presents a widely accepted treatment option for children with positional head deformities; however, studies addressing the incidence of complications during helmet therapy are rare.The current study evaluates the incidence of complications in 205 children with positional head deformity undergoing molding helmet therapy. Children were classified according to the severity of their deformity as presented by the Cranial Vault Asymmetry Index (CVAI) and the Cephalic Index (CI). Fifty-nine (28.8%) of our patients presented a moderate and 146 (71.2%) a severe form of a positional head deformity. Of these children, 166 (81.0%) were diagnosed for plagiocephaly, 19 (9.3%) were brachycephalic, and 20 (9.7%) showed a combination of plagiocephaly and brachycephaly.Overall, 54 children (26.3%) showed minor complications during their helmet molding including pressure sores (13.7%), ethanol erythema (2.9%), skin erosions/skin infections (4.3%), or deficient fitting (5.4%). Children with a combination of plagiocephaly and brachycephaly (n = 20) showed the highest risk for complications, which was significantly higher compared with children with plagiocephaly (50% vs 22.3%; P = 0.012). Irrespective of the type of positional head deformity, no statistical difference was revealed between the moderate and the severe form.Minor complications are a relatively frequent event during helmet molding therapy. Especially children with a combination of plagiocephaly-brachycephaly are at high risk for complications. A reduction of this rate might be reached by a close follow-up for a short period between helmet manufacturing adjustments.
Roles of TUP1 in Switching, Phase Maintenance, and Phase-Specific Gene Expression in Candida albicans

ABSTRACT Candida albicans strain WO-1 switches spontaneously and reversibly between a “white” and “opaque” phenotype that affects colony morphology, cellular phenotype, and expression of a number of phase-specific genes and virulence traits. To assess the role of the transcription regulator Tup1p in this phenotypic transition, both TUP1 alleles were deleted in the mutant Δtup1. Δtup1 formed “fuzzy large” colonies made up of cells growing exclusively in the filamentous form. Δtup1 cells did not undergo the white-opaque transition, but it did switch spontaneously, at high frequency (∼10−3), and unidirectionally through the following sequence of colony (and cellular) phenotypes: “fuzzy large” (primarily hyphae) → “fuzzy small” (primarily pseudohyphae) → “smooth” (primarily budding yeast) → “revertant fuzzy” (primarily pseudohyphae). Northern analysis of white-phase, opaque-phase, and hypha-associated genes demonstrated that Tup1p also plays a role in the regulation of select phase-specific genes and that each variant in the Δtup1 switching lineage differs in the level of expression of one or more phase-specific and/or hypha-associated genes. Using a rescued Δtup1 strain, in which TUP1 was placed under the regulation of the inducible MET3 promoter, white- and opaque-phase cells were individually subjected to a regime in which TUP1 was first downregulated and then upregulated. The results of this experiment demonstrated that (i) downregulation of TUP1 led to exclusive filamentous growth in both originally white- and opaque-phase cells; (ii) the white-phase-specific gene WH11 continued to be expressed in TUP1 downregulated cultures originating from white-phase cells, while WH11 expression remained repressed in TUP1-downregulated cultures originating from opaque-phase cells, suggesting that cells maintained phase identity in the absence of TUP1 expression; and (iii) subsequent upregulation of TUP1 resulted in mass conversion of originally white-phase cells to the opaque phase and maintenance of originally opaque-phase cells in the opaque phase and in the resumption in both cases of switching, suggesting that TUP1 reexpression turns on the switching system in the opaque phase.
Rothamsted Repository Download

The yield and quality of food crops is central to the well being of humans and is directly affected by climate and weather. Initial studies of climate change on crops focussed on effects of increased carbon dioxide (CO 2 ) level and/or global mean temperature and/or rainfall and nutrition on crop production. However, crops can respond nonlinearly to changes in their growing conditions, exhibit threshold responses and are subject to combinations of stress factors that affect their growth, development and yield. Thus, climate variability and changes in the frequency of extreme events are important for yield, its stability and quality. In this context, threshold temperatures for crop processes are found not to differ greatly for different crops and are important to deﬁne for the major food crops, to assist climate modellers predict the occurrence of crop critical temperatures and their temporal resolution. This paper demonstrates the impacts of climate variability for crop production in a number of crops. Increasing temperature and precipitation variability increases the risks to yield, as shown via computer simulation and experimental studies. The issue of food quality has not been given sufﬁcient importance when assessing the impact of climate change for food and this is addressed. Using simulation models of wheat, the concentration of grain protein is shown to respond to changes in the mean and variability of temperature and precipitation events. The paper concludes with discussion of adaptation possibilities for crops in response to drought and argues that characters that enable better exploration of the soil and slower leaf canopy expansion could lead to crop higher transpiration efﬁciency.
The Myth of the Holy Cow

The growth of religious fundamentalism in India is symbolized by the existence of a BJP government committed to the Hindutva. There is growing pressure to declare the cow a sacred, national animal and to ban its slaughter. This illuminating work is a response to this crazed confessionalism. It challenges obscurantist views on the sanctity of the cow in Hindu tradition and culture. Dwijendra Narayan Jha, a leading Indian historian, argues that beef played an important part in the cuisine of ancient India, long before the birth of Islam. It was very much a feature of the approved Brahmanical and Buddhist diet. The evidence he produces from a variety of religious and secular texts is compelling. His opponents, including the current government of India and the fundamentalist groups backing it, have demanded that the book should be ritually burned in public. It has already been banned by the Allahabad High Court and the author's life has been threatened.
Domain analysis of the actin-binding and actin-remodeling activities of drebrin.

Drebrin is an actin-binding protein which is expressed at highly levels in neurons. When introduced into fibroblasts, it has been known to bind to F-actin and to cause remodeling of F-actin. Here, we performed a domain analysis of the actin-binding and actin-remodeling activities of drebrin. Various fragments of drebrin cDNA were fused with green fluorescent protein cDNA and introduced into Chinese hamster ovary cells. Association of the fusion protein with F-actin and remodeling of the F-actin were examined. We found that the central 85-amino-acid sequence (residues 233-317) was sufficient for the binding to and remodeling of F-actin. The binding activity of this fragment was relatively low compared with that of full-length drebrin, but all the types of abnormalities of F-actin that are observed with full-length drebrin were also observed with this fragment. When this sequence was further fragmented, the actin-binding activity was greatly reduced and the actin-remodeling activity disappeared. The actin-binding activity of the central region of drebrin was confirmed by a cosedimentation assay of chymotryptic fragments of drebrin with purified actin. These data indicate that the actin-binding domain and actin-remodeling domain are identical and that this domain is located at the central region of drebrin.
The short-term outcome of the modified Sauvé–Kapandji procedure regarding range of motion, carpal bone translation and bony shelf size

The Sauvé–Kapandji (S–K) procedure is a common treatment for rheumatoid wrists, but in some cases severe bone destruction makes this operative modality difficult to perform, while also resulting in a poor outcome. A modified S–K procedure for these wrists has been reported, but the clinical outcomes of the modified procedure are unclear. This study evaluated 24 wrists in 20 patients who underwent the modified S–K procedure. The mean follow-up period was 34.5 months. The clinical assessments were range of motion, carpal bone translation and bony shelf size. The range of motion and carpal bone translation were similar to those produced by the S–K procedure. In regard to bony shelf size, wrists with an excessively large bony shelf tended to have a progression of carpal bone translation toward the palmar direction due to the residual malposition of the ECU tendon. The modified S–K procedure appears to be a safe and effective surgical alternative for the treatment of severely destroyed rheumatoid wrists. Although the modified procedure allows for the adjustment of the bony shelf size, it should not be used with wrists that have an excessively large bony shelf.
Regulation of herpes simplex virus true late gene expression: sequences downstream from the US11 TATA box inhibit expression from an unreplicated template

The true late genes of herpes simplex virus type 1 (HSV-1) are expressed only after the onset of viral DNA replication. Previous studies demonstrated that late promoters lack elements upstream of the TATA box and suggested that only a subset of TATA elements can function in the context of true late promoters. We determined which structural features of true late promoters are responsible for the stringent requirement for viral DNA replication by inserting a series of simple model constructs into the HSV-1 genome in place of one of the two promoters of the UL24 gene. An oligonucleotide consisting of 19 nucleotides spanning the TATA box of the HSV-1 true late US11 gene drove barely detectable levels of expression; by contrast, the corresponding regions of the Adenovirus type 2 major late promoter and the HSV-1 true late glycoprotein C promoter were much more active. Transcripts driven from all of these minimal TATA box promoters accumulated without viral DNA replication. The activity of the US11 TATA box was stimulated by adding upstream Sp1-binding sites or placing the US11 or rabbit beta-globin cap/leader region (-11 to +39) downstream. The Sp1-TATA and TATA-beta-globin cap/leader constructs remained replication independent, while the TATA-US11 cap/leader promoter displayed true late regulation. These results demonstrate that sequences located within the US11 cap/leader region impose a strict requirement for viral DNA replication on a minimal TATA box promoter.