Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of fucose and 1,2-propanediol utilization by Salmonella enterica serovar Typhimurium

After ingestion, Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters a densely populated, competitive environment in the gastrointestinal tract. To escape nutrient limitation caused by the intestinal microbiota, this pathogen has acquired specific metabolic traits to use compounds that are not metabolized by the commensal bacteria. For example, the utilization of 1,2-propanediol (1,2-PD), a product of the fermentation of L-fucose, which is present in foods of herbal origin and is also a terminal sugar of gut mucins. Under anaerobic conditions and in the presence of tetrathionate, 1,2-PD can serve as an energy source for S. Typhimurium. Comprehensive database analysis revealed that the 1,2-PD and fucose utilization operons are present in all S. enterica serovars sequenced thus far. The operon, consisting of 21 genes, is expressed as a single polycistronic mRNA. As demonstrated here, 1,2-PD was formed and further used when S. Typhimurium strain 14028 was grown with L-fucose, and the gene fucA encoding L-fuculose-1-phosphate aldolase was required for this growth. Using promoter fusions, we monitored the expression of the propanediol utilization operon that was induced at very low concentrations of 1,2-PD and was inhibited by the presence of D-glucose.
Usurpation of African Apis mellifera scutellata colonies by parasitic Apis mellifera capensis workers

La capacite des ouvrieres non fecondees a produire une descendance femelle par parthenogenese thelytoque est connue depuis longtemps chez les abeilles du Cap, Apis mellifera capensis Escholtz, race qui est confinee a l'extremite meridionale de l'Afrique. En 1990 plus de 400 colonies capensis furent apportees dans des regions occupees par l'abeille africaine arrhenotoque Apis mellifera scutellata Lepeletier. Ceci a provoque la mort de plus de 100 000 ruches exploitees, puisque les ouvrieres capensis sont capables d'usurper avec succes les colonies scutellata provoquant ainsi le deperissement et la mort de la colonie. Des etudes recentes ont montre que ces ouvrieres capensis etaient presque identiques genetiquement et formaient un « pseudo-clone ». Afin de mieux comprendre ce processus nous avons suivi 120 colonies scutellata (Tab. I) usurpees par le pseudo-clone, dont 27 d'entre elles en detail (Tab. II). Dans un cas la reine scutellata residente a coexiste pendant plus de 50 jours avec des pseudo-clones qui pondaient, mais a brusquement disparu apres seulement 1-15 jours de coexistence dans d'autres cas (Fig. 1). Les pseudo-clones ne representaient en moyenne que 22 ± 10 % de la population d'abeilles adultes d'une colonie, mais n'etaient presents dans la population de butineuses qu'a raison de 2,7 ± 1,7 %. Cela aboutissait a une quantite de plus en plus grande de couvain de pseudo-clone nourri par un nombre de plus en plus restreint d'ouvrieres scutellata. Malgre la presence de cellules de reines ayant eclos, aucune nouvelle reine, vivante ou morte, d'aucune race n'a ete observee dans aucune colonie etudiee. Il semble improbable que des reines, occasionnellement elevees a partir d'oeufs pondus par un pseudo-clone, puissent reprendre le controle d'une colonie usurpee. Lorsque des abeilles fraichement ecloses de pseudo-clones et des ouvrieres capensis normales ont ete introduites artificiellement dans une colonie scutellata ayant une reine, elles ont toutes presente des ovaires pleinement actives. Elles avaient toutes le meme âge et donc la meme chance de devenir reproductrices. Neanmoins dans les colonies de scutellata envahies, la proportion moyenne de pseudo-clones ayant des ovaires pleinement actives n'etait que de 11 ± 13 % (n = 27) ; cela laisse a penser que le developpement ovarien est inhibe chez la plupart des pseudo-clones par la presence de couvain non opercule et par d'autres pseudo-clones a ovaire pleinement actives (Fig. 2). La modelisation appliquee aux donnees obtenues par cette etude (Fig. 3) a montre que, dans une large gamme de conditions initiales, les abeilles scutellata etaient rapidement (56-105 jours) remplacees par des pseudo-clones et que la mort s'ensuivait (Tab. III et Fig. 4). Le fait que les ouvrieres capensis et les ouvrieres des pseudo-clones soient proches des reines et qu'elles possedent ce caractere unique de parthenogenese thelytoque leur permet d'usurper les colonies d'autres races d'abeilles.
The gender gap in crime is decreasing, but who’s growing equal to whom?

The declining gender gap in crime, observed in many Western countries, including Sweden, is often interpreted as showing an alarming shift in the offending of young women. Explanations to the observed pattern are often based on an assumption that women are increasingly coming to mimic the criminal behaviour of men, while we in this essay argue that to the extent behavioural change is at play, it is rather the other way around: men mimic women’s behaviour.
CYTOCHROME P450 GENE INDUCTION IN RATS EX VIVO ASSESSED BY QUANTITATIVE REAL-TIME REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION (TAQMAN)

Drug-induced changes in expression of cytochrome P450 (P450) genes are a significant issue in the preclinical development of pharmaceuticals. For example, preclinically, P450 induction can affect safety studies by reducing the systemic exposure of a compound undergoing toxicological evaluation, thus limiting the exposure that can be safely investigated in patients. Therefore, the induction potential of candidate drugs has been studied as part of the drug development process, typically using protein and/or catalytic end points. However, measuring changes in the levels of mRNA using TaqMan technology offers the opportunity to investigate this issue with the advantages of better dynamic range and specific enzyme identification. Here, we describe the TaqMan application to study ex vivo the P450 gene induction in the rat. Initially, livers from rats dosed with the prototypic P450 inducers β-napthoflavone (BNF), phenobarbital (PB), dexamethasone (DEX), and clofibric acid (CLO) were analyzed for mRNA levels of CYP1A1, 1A2, 2B1, 2B2, 2E1, 3A2, 3A23, and 4A1 and compared with control animals. The maximum fold induction of mRNA varied: 2500-fold for CYP1A1 with BNF, 680-fold for CYP2B1 with PB, 59-fold for CYP3A23 with DEX, and 16-fold for CYP4A1 with CLO. This method was then applied to estimate the inductive potential of putative drug candidates undergoing rodent toxicological evaluation. We present a summary of these data that demonstrates the sensitivity and specificity of the TaqMan assay to distinguish between inducers and noninducers and that offers a highly specific alternative to the quantification of drug effects on P450 expression using immunodetection and substrate metabolism.
Verbal Labels Modulate Perceptual Object Processing in 1-Year-Old Infants

■ Whether verbal labels help infants visually process and categorize objects is a contentious issue. Using electroencephalography, we investigated whether possessing familiar or novel labels for objects directly enhances 1-year-old infantsʼ neural processes underlying the perception of those objects. We found enhanced gamma-band (20–60 Hz) oscillatory activity over the visual cortex in response to seeing objects with labels familiar to the infant (Experiment 1) and those with novel labels just taught to the infant (Experiment 2). No such effect was observed for objects that infants were familiar with but had no label for. These results demonstrate that learning verbal labels modulates how the visual system processes the images of the associated objects and suggest a possible top–down influence of semantic knowledge on object perception. ■
Neogene Decapod Crustacea from Southern Chile

ABSTRACT Twelve species of Neogene decapod crustaceans are described from late Miocene and early Pliocene deposits in the Valdivia, Osomo-Llanquihue, and Chiloé basins as well as from Mocha Island, offshore from the Temuco Basin, southern Chile. New species of thalassinideans include Ctenocheles notialis and Axianassa? chilensis. Axianassa Schmitt, 1924, has not been reported previously in the fossil record. New species of brachyurans include Trichopeltarion frassinetti. Pirulella antipodea, Chaceon quadrata, Geryon manningi, Phenophthalmus mochaensis, and Chasmocarcinus chiloeensis. Pirulella and Phenophthalmus are new genera and Geryon Krøyer, 1837, is noted in the fossil record for the first time. Extant congeners are primarily known from lower latitude regions. Only Chaceon Manning and Holthuis, 1989, is known from the Chilean coast at present.
Sustained Oscillations of NF-κB Produce Distinct Genome Scanning and Gene Expression Profiles

NF-κB is a prototypic stress-responsive transcription factor that acts within a complex regulatory network. The signaling dynamics of endogenous NF-κB in single cells remain poorly understood. To examine real time dynamics in living cells, we monitored NF-κB activities at multiple timescales using GFP-p65 knock-in mouse embryonic fibroblasts. Oscillations in NF-κB were sustained in most cells, with several cycles of transient nuclear translocation after TNF-α stimulation. Mathematical modeling suggests that NF-κB oscillations are selected over other non-oscillatory dynamics by fine-tuning the relative strengths of feedback loops like IκBα. The ability of NF-κB to scan and interact with the genome in vivo remained remarkably constant from early to late cycles, as observed by fluorescence recovery after photobleaching (FRAP). Perturbation of long-term NF-κB oscillations interfered with its short-term interaction with chromatin and balanced transcriptional output, as predicted by the mathematical model. We propose that negative feedback loops do not simply terminate signaling, but rather promote oscillations of NF-κB in the nucleus, and these oscillations are functionally advantageous.
The Effectiveness of the Chemistry PBL Method via Facebook on the Soft Skills of College Students

It is undeniable that social media such as Facebook has such a great influence in all fields, including education. The main objective of this research is to study the interaction effects of the VARK learning style and students’ learning approach on the development of their soft skills using the Problem-Based Learning (PBL) methods via Facebook in learning chemistry. The research sample consists of 120 Kolej MARA students who were randomly selected to undergo PBL via Facebook treatment for nine weeks. This quantitative research uses experiment design with descriptive and factorial 4x2 (Two-Way ANOVA) data analysis. The descriptive data analysis result finds that the problem-based learning method via Facebook is successful in developing soft skill elements such as communication skills, teamwork and leadership skills, problem-solving skills, self-ethics and moral worth, and continuous learning and information management skills. For the Two-Way ANOVA analysis, the main effects studied are the VARK learning style and the students’ learning approach, as well as the interaction of the two towards the development of the students’ soft skills after they were involved in problem-based learning method via Facebook. Test results show that the main effect of the VARK learning style on the development of their soft skills is insignificant across the students’ learning approach using problem-based learning method via Facebook. The same goes for the main effect of the learning approach, which is also insignificant across the students’ VARK learning style. The interaction effect between both free variables (VARK learning style and learning approach) on the development of soft skills is also found to be insignificant.
Mushroom Body Output Neurons Encode Odor–Reward Associations

Neural correlates of learning and memory formation have been reported at different stages of the olfactory pathway in both vertebrates and invertebrates. However, the contribution of different neurons to the formation of a memory trace is little understood. Mushroom bodies (MBs) in the insect brain are higher-order structures involved in integration of olfactory, visual, and mechanosensory information and in memory formation. Here we focus on the ensemble spiking activity of single MB output neurons (ENs) when honeybees learned to associate an odor with reward. A large group of ENs (∼50%) changed their odor response spectra by losing or gaining sensitivity for specific odors. This response switching was dominated by the rewarded stimulus (CS+), which evoked exclusively recruitment. The remaining ENs did not change their qualitative odor spectrum but modulated their tuning strength, again dominated by increased responses to the CS+. While the bees showed a conditioned response (proboscis extension) after a few acquisition trials, no short-term effects were observed in the neuronal activity. In both EN types, associative plastic changes occurred only during retention 3 h after conditioning. Thus, long-term but not short-term memory was reflected by increased EN activity to the CS+. During retention, the EN ensemble separated the CS+ most differently from the CS− and control odors ∼140 ms after stimulus onset. The learned behavioral response appeared ∼330 ms later. It is concluded that after memory consolidation, the ensemble activity of the MB output neurons predicts the meaning of the stimulus (reward) and may provide the prerequisite for the expression of the learned behavior.
Attenuation of H-Pylori-Induced Gastric Pathology in C57bl/6 Mice by Co-Infection with Enterohepatic Helicobacters Is Helicobacter Species-Dependent

Citation Ge, Zhongming, Yang Feng, Sureshkumar Muthupalani, Laura B. Lemke, Mark T. Whary, and James G. Fox. "Attenuation of H. pylori-induced gastric pathology in C57BL/6 mice by co-infection with enterohepatic helicobacters is Helicobacter speciesdependent. " In XXIII International Workshop on Helicobacter and Related Bacteria in Chronic Digestive Inflammation and Gastric Cancer [Abstracts], Rotterdam, September 16–18, 2010, Helicobacter 15.4 (2010) p. 317.
Decreased activity in inferotemporal cortex during explicit memory: dissociating priming, novelty detection, and recognition

Studies of non-human primates have shown that activity in inferotemporal (IT) brain regions decrease over repeated stimulus exposure, a phenomenon known as repetition suppression. In the present study, repetition suppression was examined during recognition of personally experienced events (explicit memory). Brain activity was measured while subjects encoded and subsequently recognized scenic pictures. First, two recognition conditions were compared; one that mainly included familiar pictures and one that mainly included novel pictures. Responses derived from this contrast may reflect recognition memory, perceptual priming, or novelty detection. To test specifically for responses associated with recognition memory, subjects encoded a new set of pictures followed by two recognition tests. All test pictures had been presented during the course of the experiment, and the subjects identified pictures that appeared in the second encoding list. Since all pictures were familiar, repetition suppression was specifically associated with recognition memory. In the first contrast, relative change in brain activity was observed in inferotemporal, extra-striate, and hippocampal regions during recognition of familiar versus novel pictures. In the second contrast, decreased activity in IT cortex was found. The location of this region overlapped with that for the region identified in the first contrast, and a conjunction analysis showed that reduced activity in left IT cortex was common to both contrasts. These results suggest that repetition suppression in IT cortex reflects recognition memory, and that such a response is not a simple function of stimulus repetition but can be modulated by top-down processing.
Changes of endoplasmic reticulum chaperone complexes, redox state, and impaired protein disulfide reductase activity in misfolding αi‐antitrypsin transgenic mice

α1‐antitrypsin (AAT) deficiency is characterized by the accumulation of the misfolded mutant, Z form of α1‐antitrypsin (PiZ) inside the lumen of the hepatic endoplasmic reticulum (ER). Both human patients and PiZ transgenic mice have similar symptoms of hepatic failure culminating in cirrhosis and hepatocellular carcinoma. The involvement of molecular chaperones, as well as the relevance of oxidative stress in this disease is not characterized well yet. Here, we show that, in the PiZ transgenic mice, the 58‐kDa protein disulfide isomerase (PDI), the most important oxidoreductase and chaperone of the endoplasmic reticulum, is in a complex with PiZ, which is accompanied by a decrease of protein disulfide reductase activity of the ER. PiZ transgenic mice have a shift toward a more reduced ER environment and an elevation of cytoplasmic chaperones and antioxidant enzymes. Our data suggest that lower availability of PDI and a decreased protein disulfide reductase activity of the ER along with a cytoplasmic stress may contribute to the toxic effects of PiZ aggregation. —Pápp E. , Száraz P., Korcsmáros T. , and Csermely P. Changes of endoplasmic reticulum chaperone complexes, redox state, and impaired protein disulfide reductase activity in misfolding α1‐antitrypsin transgenic mice. FASEB J. 20, E235‐E244 (2006)
The Effect of Enhancing Prototype Salience on the Accuracy of Categorizing Sexual Orientation from Faces

Recent literature in person perception suggests that sexual orientation and other perceptuallyambiguous group memberships could be discerned from faces with accuracy exceeding chance levels. No study to date has explored the question of how people acquire mental representations of sexual orientation, however. In Study 1, I show that the perception of sexual orientation is distinct from that of obvious group memberships. Then, I show that people can learn prototypical representations of sexual orientation to increase their sensitivity to artificially-generated stimuli (Study 2) and to actual faces (Study 3). Last, I demonstrate that this improvement is a product of participants’ attunement to the patterns of facial features in the prototypes of the two categories. Together, the results demonstrate that people can learn mental representations of sexual orientation through exposure to environmentally relevant stimuli. Furthermore, the studies provide insights about how the mind learns social categories more generally.
Investigations on therapeutic glucocerebrosidases through paired detection with fluorescent activity-based probes

Deficiency of glucocerebrosidase (GBA) causes Gaucher disease (GD). In the common non-neuronopathic GD type I variant, glucosylceramide accumulates primarily in the lysosomes of visceral macrophages. Supplementing storage cells with lacking enzyme is accomplished via chronic intravenous administration of recombinant GBA containing mannose-terminated N-linked glycans, mediating the selective uptake by macrophages expressing mannose-binding lectin(s). Two recombinant GBA preparations with distinct N-linked glycans are registered in Europe for treatment of type I GD: imiglucerase (Genzyme), contains predominantly Man(3) glycans, and velaglucerase (Shire PLC) Man(9) glycans. Activity-based probes (ABPs) enable fluorescent labeling of recombinant GBA preparations through their covalent attachment to the catalytic nucleophile E340 of GBA. We comparatively studied binding and uptake of ABP-labeled imiglucerase and velaglucerase in isolated dendritic cells, cultured human macrophages and living mice, through simultaneous detection of different GBAs by paired measurements. Uptake of ABP-labeled rGBAs by dendritic cells was comparable, as well as the bio-distribution following equimolar intravenous administration to mice. ABP-labeled rGBAs were recovered largely in liver, white-blood cells, bone marrow and spleen. Lungs, brain and skin, affected tissues in severe GD types II and III, were only poorly supplemented. Small, but significant differences were noted in binding and uptake of rGBAs in cultured human macrophages, in the absence and presence of mannan. Mannan-competed binding and uptake were largest for velaglucerase, when determined with single enzymes or as equimolar mixtures of both enzymes. Vice versa, imiglucerase showed more prominent binding and uptake not competed by mannan. Uptake of recombinant GBAs by cultured macrophages seems to involve multiple receptors, including several mannose-binding lectins. Differences among cells from different donors (n = 12) were noted, but the same trends were always observed. Our study suggests that further insight in targeting and efficacy of enzyme therapy of individual Gaucher patients could be obtained by the use of recombinant GBA, trace-labeled with an ABP, preferably equipped with an infrared fluorophore or other reporter tag suitable for in vivo imaging.
Multiple Instance Learning with Query Bags

In many machine learning applications, precisely labeled data is either burdensome or impossible to collect. Multiple Instance Learning (MIL), in which training data is provided in the form of labeled bags rather than labeled instances, is one approach for dealing with ambiguously labeled data. In this paper we argue that in many applications of MIL (e.g. image, audio, text, bioinformatics) a single bag actually consists of a large or infinite number of instances, such as all points on a low dimensional manifold. For practical reasons, these bags get subsampled before training. Instead, we introduce a MIL formulation which directly models the underlying structure of these bags. We propose and analyze the query bag model, in which instances are obtained by repeatedly querying an oracle in a way that can capture relationships between instances. We show that sampling more instances results in better classification performance, which motivates us to develop algorithmic strategies for sampling many instances while maintaining efficiency.
A Semi-Supervised Learning Algorithm for Multi-Layered Perceptrons

We address the issue of learning multi-layered perceptrons (MLPs) in a discriminative, inductive, multiclass, parametric, and semi-supervised fashion. We introduce a novel objective function that, when optimized, simultaneously encourages 1) accuracy on the labeled points, 2) respect for an underlying graph-represented manifold on all points, 3) smoothness via an entropic regularizer of the classifier outputs, and 4) simplicity via an ‘2 regularizer. Our approach provides a simple, elegant, and computationally efficient way to bring the benefits of semi-supervised learning (and what is typically an enormous amount of unlabeled training data) to MLPs, which are one of the most widely used pattern classifiers in practice. Our objective has the property that efficient learning is possible using stochastic gradient descent even on large datasets. Results demonstrate significant improvements compared both to a baseline supervised MLP, and also to a previous non-parametric manifold-regularized reproducing kernel Hilbert space classifier.