Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions between fetal rat brain cells and mature brain tissue in vivo and in vitro

Fetal as well as mature neural cells were homografted into the right cerebral hemisphere of adult BD–IX rats. The animals were sacrificed 7 d after implantation, and the localization of implanted cells was visualized by fluorescence and light microscopy. The cell implants were prestained with the fluorescent vital dye 1,1′‐Dioctadecyl –3,3,3′3′‐tetramethylindocarbocyanine perchlorate (Dil) to discriminate between implanted cells and host brain tissue. At the implantation site, the fetal brain cells as well as the cells from immature brain cell aggregates showed diffuse infiltration into the surrounding host brain tissue of up to 0.5 mm. Extensive cell migration along the corpus callosum for up to 5 mm in the coronal and to a lesser extent in the sagittal plane was also observed. In addition, fetal cells were distributed in the subarachnoid space of both cerebral hemispheres and showed a distinct association with larger blood vessels. Cells from mature brain aggregates did not migrate as far as fetal cells and showed only a local infiltration into the host neuropil. Fluorescent microspheres as well as fixed fetal brain cells were implanted, either alone or in combination with vital cells to distin guish between active cell migration and passive cell displacement. The microspheres and the fixed cells were found either localized to the implantation pathway or distributed in the corpus callosum for up to 2 mm in the coronal plane without any dispersion in the sagittal plane. The microspheres also showed an extensive displacement in the subarachnoid space. In vitro co–culture experiments between two immature aggregates showed a complete fusion of the two aggregates during a 96 h culture period. In co–cultures between two mature aggregates complete fusion was not prominent, although the confrontation zone appeared diffuse. Confrontations between a mature and an immature aggregate showed the same pattern of interaction as seen for the two mature aggregates. It is concluded that carbocyanine dyes may be used as a tracer for transplanted cells. Cells from fetal rat brain cell aggregates, opposed to those from mature aggregates, showed extensive migration along well defined anatomical structures in the mature brain. Some of the spread of cells following implantation is probably due to passive movement since inert microspheres will spread into certain areas of the CNS.
Coevolution of the ATPase ClpV, the Sheath Proteins TssB and TssC, and the Accessory Protein TagJ/HsiE1 Distinguishes Type VI Secretion Classes*

Background: The bacterial type VI secretion apparatus is a phage tail-like structure that secretes toxins/effectors. Results: Four components of the type VI secretion system have coevolved and interact. Conclusion: Distinct classes of type VI secretion systems emerge from the phylogenetic data. Significance: Molecular understanding of type VI secretion might make it amenable to targeting by antimicrobials. The type VI secretion system (T6SS) is a bacterial nanomachine for the transport of effector molecules into prokaryotic and eukaryotic cells. It involves the assembly of a tubular structure composed of TssB and TssC that is similar to the tail sheath of bacteriophages. The sheath contracts to provide the energy needed for effector delivery. The AAA+ ATPase ClpV disassembles the contracted sheath, which resets the systems for reassembly of an extended sheath that is ready to fire again. This mechanism is crucial for T6SS function. In Vibrio cholerae, ClpV binds the N terminus of TssC within a hydrophobic groove. In this study, we resolved the crystal structure of the N-terminal domain of Pseudomonas aeruginosa ClpV1 and observed structural alterations in the hydrophobic groove. The modification in the ClpV1 groove is matched by a change in the N terminus of TssC, suggesting the existence of distinct T6SS classes. An accessory T6SS component, TagJ/HsiE, exists predominantly in one of the classes. Using bacterial two-hybrid approaches, we showed that the P. aeruginosa homolog HsiE1 interacts strongly with ClpV1. We then resolved the crystal structure of HsiE1 in complex with the N terminus of HsiB1, a TssB homolog and component of the contractile sheath. Phylogenetic analysis confirmed that these differences distinguish T6SS classes that resulted from a functional co-evolution between TssB, TssC, TagJ/HsiE, and ClpV. The interaction of TagJ/HsiE with the sheath as well as with ClpV suggests an alternative mode of disassembly in which HsiE recruits the ATPase to the sheath.
Long‐term enhancement of CA1 synaptic transmission is due to increased quantal size, not quantal content

Quantal components of Schaffer collateral synaptic transmission recorded intracellularly from CA1 pyramidal cells were examined using 2 methods: simultaneous recordings of CA3‐CA1 cell‐pairs, and minimal electrical stimulation in stratum radiatum. Quantal parameters estimated by the method of failures and by a computer algorithm that optimized parameter estimates using deconvolution of background noise were highly correlated. EPSP‐amplitude histograms of CA3‐CA1 cell pairs (N = 10) and minimal electrical stimulation (N = 33) could be adequately described either by Poisson or binomial statistics, or by both, and exhibited similar estimates of unit quantal size (q) and mean quantal content (m). Paired‐pulse stimulation with 50 msec between stimuli resulted in an expected facilitation in the EPSP amplitude and increase in m during the second response, as estimated by noise deconvolution, by the decrease in apparent failures, and by a decrease in the coefficient of variation of the EPSP. Tetanization of the Schaffer collaterals that induced long‐term enhancement (LTE/LTP) of the population response was associated with an average increase in q for minimal‐stimulation responses, with no significant change in any estimate of m. Taken together, these data indicate that, under the present experimental conditions, LTE is expressed as an increase in quantal size, rather than an increase in the number of quanta released per presynaptic impulse. Although this is not definitive evidence for a postsynaptic mechanism, these findings do further restrict the classes of possible presynaptic mechanisms that may be proposed to account for LTE expression.
Expression of HNFs and C/EBPα is correlated with immunocytochemical differentiation of cell lines derived from human hepatocellular carcinomas, hepatoblastomas and immortalized hepatocytes

Objective assessment of the differentiation grade of hepatocellular carcinomas (HCCs) is important for evaluation of the pathological diagnosis, prognosis and therapeutic treatment. Differentiation of hepatocytes is reflected by their expression of hepatic functional proteins in the mouse embryo, and liver‐enriched transcription factors (LETFs) have been shown to regulate hepatic functional genes strictly. Previous reports demonstrated that the level of LETF expression is altered in HCC or preneoplastic nodules compared with noncancerous tissues. Therefore, LETF expression levels might be useful as a measure of HCC maturation. In this study, to clarify the correlation between the expression of LETFs and the differentiation grade of HCCs, we performed a quantitative analysis of the mRNA expressions of HNFs and C/EBPα using real‐time reverse‐transcription PCR and immunocytochemical analysis for hepatic functional proteins in twelve cell lines. Furthermore, we examined orthotopic transplantations of the HCC cell lines in C.B‐17/Icrj‐scid/scid mice and characterized the histologic and cytologic differentiation of the tumors that developed. Our results showed that comprehensive expressions of HNF‐3β, HNF‐4α, HNF‐1α, and C/EBPα were specific to HCCs with well‐differentiated function and morphology. Furthermore, among these four transcription factors, HNF‐4α and HNF‐1α expressions showed synchronism and had a close relation with HCC differentiation. These in vitro results were confirmed in tumors developed in SCID mice in vivo. These findings suggested that HNF‐4α and HNF‐1α are useful markers to assess the degree of HCC differentiation, which we suggest could be evaluated objectively by the quantitative analysis of HNFs and C/EBPα in HCCs.
The ideologies of teachers and parents regarding family-school relationships in urban elementary schools: a case study.

Parental involvement is associated with students’ educational achievement (Ahmad, 2010; Theodorou, 2008; Yanghee, 2009). Although parent involvement is linked to student success, schools frequently fail to establish a strong connection between home and school (Ahmad, 2010; Bourdieu, 1973; Brint, 2011), particularly in urban areas (Epstein & Sanders, 2006). Thus, a descriptive case study was used to examine the ideologies of both teachers and parents regarding the quality of their interrelationships with respect to how they both care for their children. Three varied data sets were used: (a) open-ended interviews, (b) field notes, and (c) a focus group. The data from the three sources were analyzed and coded using MAXQDA data analysis software. Results indicated that both teachers and parents prioritize communication and sharing information as two main strategies to improve engagement and optimize children’s academic results. Additionally, results indicated that both groups expressed the hope that parental involvement in their children’s educations would lead to better parent–teacher relationships and the children’s continued motivation for learning. Further, results indicated four major social and cultural factors that influence the relationships between families and schools: attitudes and beliefs, unwelcome feelings due to a new school policy, gaps in home–school communication, and a lack of trust in special services. Moreover, creating a welcoming environment, improving home–school communication, and establishing early collaboration emerged as significant requirements for healthy parent–teacher relationships.
Male germ cell apoptosis: regulation and biology

Cellular apoptosis appears to be a constant feature in the adult testis and during early development. This is essential because mammalian spermatogenesis is a complex process that requires precise homeostasis of different cell types. This review discusses the latest information available on male germ cell apoptosis induced by hormones, toxins and temperature in the context of the type of apoptotic pathway either the intrinsic or the extrinsic that may be used under a variety of stimuli. The review also discusses the importance of mechanisms pertaining to cellular apoptosis during testicular development, which is independent of exogenous stimuli. Since instances of germ cell carcinoma have increased over the past few decades, the current status of research on apoptotic pathways in teratocarcinoma cells is included. One other important aspect that is covered in this review is microRNA-mediated control of germ cell apoptosis, a field of research that is going to see intense activity in near future. Since knockout models of various kinds have been used to study many aspects of germ cell development, a comprehensive summary of literature on knockout mice used in reproduction studies is also provided.
Root dilation in patients with truncus arteriosus.

OBJECTIVE A dilated aortic root is a common finding in children and adults with some forms of congenital heart defects. No data exist on root dilation in truncus arteriosus. We sought to delineate root dimensions across a population of patients with truncus arteriosus. DESIGN We performed a single-center retrospective review of all patients with truncus arteriosus. Demographic information, clinical history, and most recent echocardiographic data were evaluated. RESULTS We identified 76 patients whose most recent study was at a median age of 5.4 years (range 0--32.7 years). Mean truncal root z-score was 5.1 ± 2.3. All but three patients had truncal root z-scores greater than or equal to 2. Truncal root z-scores remained stable with increasing body surface area and age. There were no cases of dissection or rupture. Six patients underwent truncal root surgery, typically for indications of root dilation with significant truncal valve insufficiency and left ventricular dilation. CONCLUSIONS In conclusion, mean truncal root z-score was 5, and all but three patients had truncal root z-scores greater than or equal to 2. Although repeat surgical intervention was rare and major complications related to root dilation did not occur in our cohort, further studies with longitudinal follow-up into adulthood are needed.
Vps1p, a member of the dynamin GTPase family, is necessary for Golgi membrane protein retention in Saccharomyces cerevisiae.

The KEX2‐encoded endoprotease of Saccharomyces cerevisiae resides in the Golgi complex where it participates in the maturation of alpha‐factor mating pheromone precursor. Clathrin heavy chain gene disruptions cause mislocalization of Kex2p to the cell surface and reduce maturation of the alpha‐factor precursor. Based on these findings, a genetic screen has been devised to isolate mutations that affect retention of Kex2p in the Golgi complex. Two alleles of a single genetic locus, lam1 (lowered alpha‐factor maturation), have been isolated, which result in inefficient maturation of alpha‐factor precursor. In lam1 cells, Kex2p is not mislocalized to the cell surface but is abnormally unstable. Normal stability is restored by the pep4 mutation which reduces the activity of vacuolar proteases. In contrast, the pheromone maturation defect is not corrected by pep4. Organelle fractionation by sucrose density gradient centrifugation shows that Kex2p is not retained in the Golgi complex of lam1 cells. Vacuolar protein precursors are secreted by lam1 mutants, revealing another sorting defect in the Golgi complex. Genetic complementation reveals that lam1 is allelic to the VPS1 gene, which encodes a dynamin‐related GTPase. These results indicate that Vps1p is necessary for membrane protein retention in a late Golgi compartment.
Productivity Distribution and Economic Growth

This paper develops a tractable model of economic growth in which heterogeneous households produce capital a la Romer (1986). The paper demonstrates that depending on its varying degrees of persistence, productivity heterogeneity dictates economic growth. A regression analysis based upon a reduced-form version of the model shows that the persistence of human capital is the driving force behind the positive effects of productivity dispersion on economic growth
The Long-Run Dynamics of Electricity Demand: Evidence From Municipal Aggregation

We study the dynamics of residential electricity demand by exploiting a natural experiment that produced large and long-lasting price changes in over 250 Illinois communities. Using a flexible difference-in-difference matching approach, we estimate that the price elasticity of demand grows from − 0.09 in the first six months to − 0.27 two years later. We find similar results with a dynamic model in which usage is a function of past and future prices. Our findings highlight the importance of accounting for consumption dynamics when evaluating energy policy. (JEL L94, L98, Q41, Q48)
Evaluation of pH at the Bacteria–Dental Cement Interface

Physiochemical assessment of the parasite-biomaterial interface is essential in the development of new biomaterials. The purpose of this study was to develop a method to evaluate pH at the bacteria-dental cement interface and to demonstrate physiochemical interaction at the interface. The experimental apparatus with a well (4.0 mm in diameter and 2.0 mm deep) was made of polymethyl methacrylate with dental cement or polymethyl methacrylate (control) at the bottom. Three representative dental cements (glass-ionomer, zinc phosphate, and zinc oxide-eugenol cements) were used. Each specimen was immersed in 2 mM potassium phosphate buffer for 10 min, 24 hrs, 1 wk, or 4 wks. The well was packed with Streptococcus mutans NCTC 10449, and a miniature pH electrode was placed at the interface between bacterial cells and dental cement. The pH was monitored after the addition of 1% glucose, and the fluoride contained in the cells was quantified. Glass-ionomer cement inhibited the bacteria-induced pH fall significantly compared with polymethyl methacrylate (control) at the interface (10 min, 5.16 ± 0.19 vs. 4.50 ± 0.07; 24 hrs, 5.20 ± 0.07 vs. 4.59 ± 0.11; 1 wk, 5.34 ± 0.14 vs. 4.57 ± 0.11; and 4 wks, 4.95 ± 0.27 vs. 4.40 ± 0.14), probably due to the fluoride released from the cement. This method could be useful for the assessment of pH at the parasite-biomaterial interface.
Localization of cranin (dystroglycan) at sites of cell-matrix and cell-cell contact: recruitment to focal adhesions is dependent upon extracellular ligands.

We report that cranin (dystroglycan) can become recruited to focal adhesions of cultured rat REF 52 fibroblasts and human aortic smooth muscle cells. Within mature focal adhesions, cranin was present within the plaque region defined by beta 1 integrin, vinculin and phosphotyrosine staining, but occupied a larger domain corresponding to the terminal segments of stress fibers that was more precisely co-extensive with the cytoskeletal proteins alpha-actinin, utrophin and aciculin. When REF 52 fibroblasts were plated on different substrata in the absence of protein synthesis and secretion in serum-free medium, focal clusters of cranin readily formed within 2 hours on matrix proteins that bind cranin directly (laminin or agrin) which were maintained as the focal adhesions became mature. In contrast, cranin failed to become targeted to cell-substratum attachment sites, either at early or later times, when cells were plated on a variety of other substrata that elicit formation of focal adhesions but do not bind cranin directly (fibronectin, vitronectin, collagen type IV, or anti-beta 1 integrin antibody TS2/16). These data strongly suggest that targeting of cranin to focal adhesions was dependent upon the presence of an extracellular ligand capable of binding cranin directly. However, some cultured nonmuscle cell lines (e.g., human umbilical vein endothelial cells, NIH 3T3 and CHO cells) failed to localize cranin to focal adhesions, even when plated on laminin. Cranin was also enriched at cell-cell adherens-type junctions of human normal breast MCF-10 epithelial cells, and at growth cones of E17 rat hippocampal axons. That cranin can become targeted to sites of cell-cell and cell-substratum contact in diverse cell types supports the hypothesis that cranin may be involved in mediating or regulating cell adhesion. The absence of muscle-specific and synapse-specific proteins within fibroblasts and epithelial cells provides a different context for thinking about cranin (dystroglycan) that may aid in discerning general principles of its structure and function.
Critical analysis of encounter traces

The limitations of contact-logging experiments, particularly those based on periodic Bluetooth neighborhood scans, prevent them from detecting many contact opportunities. This paper highlights recent results on inferring a plausible movement from contact traces and shows how they may be used to identify those missed contacts. This analysis is then applied to the Rollernet contact trace and indicates that these missed contacts have an important impact on protocol performance evaluation.
Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanism

Nonfibrillar soluble oligomers, which are intermediates in the transition from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. To monitor the early events that direct assembly of amyloidogenic peptides we probe the dynamics of formation of (Aβ16–22)n by adding a monomer to a preformed (Aβ16–22)n−1 (n = 4–6) oligomer in which the peptides are arranged in an antiparallel β-sheet conformation. All atom molecular dynamics simulations in water and multiple long trajectories, for a cumulative time of 6.9 μs, show that the oligomer grows by a two-stage dock–lock mechanism. The largest conformational change in the added disordered monomer occurs during the rapid (≈50 ns) first dock stage in which the β-strand content of the monomer increases substantially from a low initial value. In the second slow-lock phase, the monomer rearranges to form in register antiparallel structures. Surprisingly, the mobile structured oligomers undergo large conformational changes in order to accommodate the added monomer. The time needed to incorporate the monomer into the fluid-like oligomer grows even when n = 6, which suggests that the critical nucleus size must exceed six. Stable antiparallel structure formation exceeds hundreds of nanoseconds even though frequent interpeptide collisions occur at elevated monomer concentrations used in the simulations. The dock–lock mechanism should be a generic mechanism for growth of oligomers of amyloidogenic peptides.
A bacteriocin produced by certain M-type 49 Streptococcus pyogenes strains when incubated anaerobically

Summary Bacteriocin production (P)-typing of 75 M-type 49 group-A streptococci obtained from a variety of epidemiological incidents in different countries gave no evidence of production under the usual aerobic test conditions. However, with anaerobic incubation, 28% of the strains gave a pattern of inhibitory activity against the indicator strains which was indistinguishable from that previously attributed to the bacteriocin, streptococcin A-FF22 (SA-FF22). Isolation and partial purification of the M type 49 bacteriocin (SA-M49) by freeze–thaw elution from anaerobically grown lawn cultures, followed by ammonium sulphate precipitation and Sephadex chromatography, showed the activity to be associated with a heat-stable proteinaceous molecule of molecular weight approximately 8000 – properties similar to those of SA-FF22. SA-FF22 and SA-M49 were found to have identical inhibitory spectra including immunity of the producer strains to the inhibitory activity of both the homologous and heterologous bacteriocin preparations. SA-M49 production occurred in some strains of phage subtypes II, III and provisional VI and. since it was a consistent property for all isolates from single outbreaks of infection, it provides a means of discriminating between strains of each of these three phage subtypes. There was no evidence of any increased incidence of SA-M49 production in M-type 49 strains associated with nephritic sequelae
Helicobacter pylori Outer Membrane Vesicles Modulate Proliferation and Interleukin-8 Production by Gastric Epithelial Cells

ABSTRACT Helicobacter pylori infection, which is always associated with gastritis, can progress to ulceration or malignancy. The diversity in clinical outcomes is partly attributed to the expression of virulence factors and adhesins by H. pylori. However, H. pylori may not have to adhere to the epithelium to cause gastritis. We hypothesize that outer membrane vesicles (OMV), which are constantly shed from the surface of H. pylori, play a role as independent activators of host cell responses. In this study, we found that low doses of OMV from cag PAI+ toxigenic and cag PAI− nontoxigenic strains increased proliferation of AGS gastric epithelial cells. At higher doses, we detected growth arrest, increased toxicity, and interleukin-8 (IL-8) production. The only strain differences detected were vacuolation with the toxigenic strain and higher levels of IL-8 production with OMV from the cag PAI− nontoxigenic strain. In summary, we suggest that constitutively shed OMV play a role in promoting the low-grade gastritis associated with H. pylori infection.