Miracle-dz/UniFAR-FTUs huggingface dataset:
Clear Cell Papillary Renal Cell Carcinoma–like Tumors in Patients With Von Hippel-Lindau Disease Are Unrelated to Sporadic Clear Cell Papillary Renal Cell Carcinoma

Clear cell papillary renal cell carcinoma (CCPRCC) shares morphologic overlap with clear cell renal cell carcinoma, although it lacks chromosome 3p and VHL gene abnormalities. Rare cases have been reported in von Hippel-Lindau (VHL) patients (germline mutation of the VHL gene), the significance of which is uncertain. We analyzed morphologic, immunohistochemical, and molecular features in 14 CCPRCC-like tumors and 13 clear cell renal cell carcinomas from 12 patients with VHL disease. Gross appearance of CCPRCC-like tumors ranged from yellow-orange to tan, red-brown, or extensively cystic. Histologic features included: small papillary tufts (79%), branched tubules (71%), branched papillae (64%), flattened peripheral cysts (64%), and apically aligned nuclei (43%). Almost all CCPRCC-like tumors (82%) lacked the characteristic immunoprofile of sporadic CCPRCC (CK7+, CAIX+, CD10−, AMACR−), often showing diffuse CD10 labeling (64%), negative or focal CK7 reactivity (55%), or both (18%). Three tumors (27%) showed strong AMACR staining. Chromosome 3p deletion was often present (82%), similar to that observed in clear cell renal cell carcinomas (80%); no CCPRCC-like tumor had chromosome 7 or 17 abnormalities. In summary, tumors that histologically resemble CCPRCC sometimes occur in patients with VHL disease but usually lack the characteristic immunohistochemical and molecular profile, suggesting that they do not share the same pathogenesis.
Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific

Deep-sea hydrothermal vent fields are areas on the seafloor with high biological productivity fueled by microbial chemosynthesis. Members of the Aquificales genus Persephonella are obligately chemosynthetic bacteria, and appear to be key players in carbon, sulfur, and nitrogen cycles in high temperature habitats at deep-sea vents. Although this group of bacteria has cosmopolitan distribution in deep-sea hydrothermal ecosystem around the world, little is known about their population structure such as intraspecific genomic diversity, distribution pattern, and phenotypic diversity. We developed the multi-locus sequence analysis (MLSA) scheme for their genomic characterization. Sequence variation was determined in five housekeeping genes and one functional gene of 36 Persephonella hydrogeniphila strains originated from the Okinawa Trough and the South Mariana Trough (SNT). Although the strains share >98.7% similarities in 16S rRNA gene sequences, MLSA revealed 35 different sequence types (ST), indicating their extensive genomic diversity. A phylogenetic tree inferred from all concatenated gene sequences revealed the clustering of isolates according to the geographic origin. In addition, the phenotypic clustering pattern inferred from whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis can be correlated to their MLSA clustering pattern. This study represents the first MLSA combined with phenotypic analysis indicative of allopatric speciation of deep-sea hydrothermal vent bacteria.
Structural and dielectric characterization of SrTio/sub 3/ and BST thin films for microwave applications

Heteroepitaxial SrTiO/sub 3/ and polycrystalline Ba/sub (1-x)/Sr/sub x/TiO/sub 3/ (x = 0.35, 0.40, 0.50) thin films (/spl sim/300 nm) were deposited on [100] oriented LaAlO/sub 3/ single crystal substrates by pulsed laser deposition using a KrF excimer laser (/spl lambda/ = 248 nm). RBS, XRD, FESEK and AFM were used for structural characterization. The stoichiometry was found to be closest to ideal at higher temperatures around 750/spl deg/C. The SrTiO/sub 3/ films were confirmed to be epitaxial with XRD omega scans, while the BST films were polycrystalline. The permittivity and loss tangent of the films were measured in the range of 1 kHz to 1 MHz. Both materials showed a high dielectric constant 230 for ST and around 800 for BST at room temperature, with losses on the order of a few percent. The tunability of BST was also measured and found to be up to 35%, depending on composition. In addition, correlations between film morphology, processing conditions, and stoichiometry are discussed.
Microstructures of Zr-Added Co-Cr-Mo Alloy Compacts Fabricated with a Metal Injection Molding Process and Their Metal Release in 1 mass% Lactic Acid

The microstructures of Zr-added Co-29Cr-6Mo alloy compacts fabricated with a metal injection molding (MIM) process and their metal release from the compacts immersed in 1% lactic acid were investigated for medical applications. The relationship between the microstructure and amount of Co released from the compacts is discussed phenomenologically. The relative density of the Co-29Cr-6Mo compacts increased when Zr was added to the powder with amounts of 0.03 and 0.1 mass% and sintered in Ar or N 2 . The amounts of Co released from the compacts containing 0.03 and 0.1 mass% Zr sintered in Ar or N 2 were smaller than those from the other compacts. Therefore, the addition of Zr to the Co-29Cr-6Mo powders enhanced the sintering of the compacts and decreased the porosity in the resultant products, leading to the suppression of the Co release from the compacts. When the Zr-added Co-29Cr-6Mo alloy powders were sintered in N 2 , the relative density of the compacts was smaller than that of those sintered in Ar. The powders were nitrided during sintering in N 2 , and the nitrides disturbed the densification during sintering. In addition, a lamellar structure was formed in the Co-29Cr-6Mo and Co-29Cr-6Mo-0.5Zr compacts. The amount of Co released from these compacts was larger than that released from the other compacts because local corrosion occurred at the interface between the different phases in these compacts during immersion in 1% lactic acid. In the MIM process, a small addition of Zr (less than 0.1 mass%) to the Co-29Cr-6Mo alloy is effective for densification during sintering and suppression of the Co release from the compacts.
Increased Immunosuppression, Not Anticoagulation, Extends Cardiac Xenograft Survival

Background. Cardiac xenograft function is lost due to delayed xenograft rejection (DXR) characterized by microvascular thrombosis and myocardial necrosis. The cause of DXR is unknown but may result from thrombosis induced by antibody-mediated activation of endothelial cells and/or by incompatibilities in thromboregulatory interactions. Methods. To examine these issues, a series (Groups 1–6) of previous transgenic CD46 pig-to-baboon heterotopic cardiac transplants were reanalyzed for baseline immunosuppressive levels, graft survival and infectious complications with and without systemic anticoagulation. Groups 1–4 received low dose tacrolimus and sirolimus maintenance therapy, with splenectomy, anti-CD20 and daily α-Gal polymer. Group 1 recipients received no anticoagulation. Groups 2–4 were anticoagulated with aspirin and Plavix, Lovenox, or Coumadin, respectively. Group 5 was treated with Lovenox and high dose tacrolimus and sirolimus maintenance therapy. Group 6 recipients received no postoperative anticoagulation but the same immunosuppression as group 5. Results. Median survival (15–22 days) within groups 1–4 was not significantly different. At rejection all tissues exhibited microvascular thrombosis, coagulative necrosis and similar levels of platelet and fibrin deposition. Groups 5 and 6 median survival (76 days) was significantly increased compared to groups 1–4. There was no significant difference in median survival between Lovenox treated recipients (68 days) and anticoagulant free recipients (96 days). Rejected tissues showed vascular antibody deposition, microvascular thrombosis, and myocyte necrosis. Conclusion. Significant prolongation in xenograft survival is achieved by improved immunosuppression. These results suggest that ongoing immune responses remain the major stimulus for DXR.
Grassmannian Packings for Efficient Quantization in MIMO Broadcast Systems

It is well known that availability of the channel state information (CSI) at the transmitter significantly increases the throughput of MIMO broadcast systems. For even larger increase of the throughput it is important to identify and to transmit to receivers whose channel vectors are almost orthogonal to each other. Since typically the feedback link from the receivers to the transmitter is low-rate, only a quantized version of the CSI can be sent back to the transmitter. In this paper we consider the problem of designing Grassmannian packings that can serve as good quantization codebooks, have low maximum likelihood decoding complexity, and allow to identify receivers with orthogonal, and/or almost orthogonal, channel vectors in a very efficient way.
Stored Representations of three-Dimensional Objects in the Absence of Two-Dimensional Cues

Object recognition was studied in human subjects to determine whether the storage of the visual objects was in a two-dimensional or a three-dimensional representation. Novel motion-based and disparity-based stimuli were generated in which three-dimensional and two-dimensional form cues could be manipulated independently. Subjects were required to generate internal representations from motion stimuli that lacked explicit two-dimensional cues. These stored internal representations were then matched against internal three-dimensional representations constructed from disparity stimuli. These new stimuli were used to confirm prior studies that indicated the primacy of two-dimensional cues for view-based object storage. However, under tightly controlled conditions for which only three-dimensional cues were available, human subjects were also able to match an internal representation derived from motion to that of disparity. This last finding suggests that there is an internal storage of an object's representations in three dimensions, a tenet that has been rejected by view-based theories. Thus, any complete theory of object recognition that is based on primate vision must incorporate three-dimensional stored representations.
THE KINETICS OF IRON METABOLISM IN NORMAL GROWING SWINE

Plasma and red cell iron turnover rates were determined in 18 normal growing swine by the use of tracer doses of Fe59. Body surface counting was performed on a representative group of animals following the injection of the isotope. The mean half-time of plasma iron disappearance was 1.19 ± 0.26 hours. Two exponential rates of disappearance of Fe59 from the plasma were observed in 15 of the pigs and a single rate was observed in the other 3. The mean plasma iron turnover rate was 1.11 ± 0.34 mg. /kg. day. The average maximum incorporation of Fe59 into the erythrocytes was 92 ± 9 per cent. The mean red cell iron incorporation rate was 1.10 mg. /kg. day, but an average of 0.42 mg. /kg. day of this was calculated as being due to increasing red cell mass incidental to body growth, so that the true mean red cell iron turnover rate was 0.59 ± 0.19 mg. /kg. day. The average "apparent" red cell life span was 63 ± 16 days. This is in agreement with the red cell life span of 62 days determined previously with glycine-2-C14.
Typhoid fever: hurdles to adequate hand washing for disease prevention among the population of a peri-urban informal settlement in Fiji.

PROBLEM/CONTEXT The Pacific island nation of Fiji Islands has high rates of endemic typhoid fever which is difficult to diagnose and often underreported. However, the majority of cases are preventable through use of safe water; adequate sanitation; vaccination; and, most sustainable of all, simple hygienic behaviour, such as hand washing with soap (HWWS). Despite many attempts by public health authorities, little progress has been made in the area of environmental adaptation and behaviour change. ACTION To explore perceptions of typhoid fever risk among urban squatters and behavioural determinants surrounding HWWS, indigenous Fijians living in informal settlements with high typhoid fever incidence were invited to participate in focus group discussions. In-depth interviews were conducted with community leaders. OUTCOME Perceptions of typhoid fever suggest confusion about risk factors, symptoms and communicability. Environmental barriers for hand washing were related to water and soap access. Standard social marketing approaches have been trialled with little clear evidence of impact. Despite this, we continue to advocate for the social and cultural determinants of typhoid prevention to remain central to future public health strategies. DISCUSSION Despite behaviour change being notoriously difficult, we argue that community-driven behaviour adaptation initiatives based on sound epidemiological evidence and health communication theory are likely to have significant impact and greater likelihood of sustainability.
Towards episodic memory-based long-term affective interaction with a human-like robot

In this paper, we address the question of how to create episodic memory based long-term affective interactions with a human-like robot. A key challange for long-term interaction is the recall of past important events during conversation. We suggest that episodic memory is a core concept for realizing this intelligence. In this paper, we propose a model of episodic memory and integrate it with a decision making module based on a Hierarchical Task Network (HTN) planner. Plans generated by the HTN planner are executed by a Finite-state-machine (FSM) based dialogue system in order to produce appropriate responses. Finally, we present a prototype implementation demonstrating the preliminary results we obtained.
A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing

Summary The single‐stranded, positive‐sense RNA genome of viruses in the genus Potyvirus encodes a large polyprotein that is cleaved to yield 10 mature proteins. The first three cleavage products are P1, HCpro and P3. An additional short open reading frame (ORF), called pipo, overlaps the P3 region of the polyprotein ORF. Four related potyviruses infecting sweet potato (Ipomoea batatas) are predicted to contain a third ORF, called pispo, which overlaps the 3′ third of the P1 region. Recently, pipo has been shown to be expressed via polymerase slippage at a conserved GA6 sequence. Here, we show that pispo is also expressed via polymerase slippage at a GA6 sequence, with higher slippage efficiency (∼5%) than at the pipo site (∼1%). Transient expression of recombinant P1 or the ‘transframe’ product, P1N‐PISPO, in Nicotiana benthamiana suppressed local RNA silencing (RNAi), but only P1N‐PISPO inhibited short‐distance movement of the silencing signal. These results reveal that polymerase slippage in potyviruses is not limited to pipo expression, but can be co‐opted for the evolution and expression of further novel gene products.
Fis1p and Caf4p, but not Mdv1p, determine the polar localization of Dnm1p clusters on the mitochondrial surface

The mitochondrial division machinery consists of the large dynamin-related protein Dnm1p (Drp1/Dlp1 in humans), and Fis1p, Mdv1p and Caf4p. Proper assembly of Dnm1p complexes on the mitochondrial surface is crucial for balanced fission and fusion events. Using quantitative confocal microscopy, we show that Caf4p is important for the recruitment of Dnm1p to the mitochondria. The mitochondrial Dnm1p assemblies can be divided into at least two morphologically distinguishable fractions. A small subset of these assemblies appear to be present as Dnm1p-spirals (or rings) that encircle tubule constrictions, with seldom more than seven turns. A larger fraction of the Dnm1p assemblies is primarily present at one side of the mitochondrial tubules. We show that a majority of these mitochondria-associated Dnm1p clusters point towards the cell cortex. This polarized orientation is abolished in fis1Δ and caf4Δ yeast cells, but is maintained in mdv1Δ cells and after disruption of the actin cytoskeleton. This study suggests that Caf4p plays a key role in determining the polarized localization of those Dnm1p clusters that are not immediately involved in the mitochondrial fission process.
Counterpart Theory and Quantified Modal Logic

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The role of experience in children’s discrimination of unfamiliar languages

Five- and six-year-old children (n = 160) participated in three studies designed to explore language discrimination. After an initial exposure period (during which children heard either an unfamiliar language, a familiar language, or music), children performed an ABX discrimination task involving two unfamiliar languages that were either similar (Spanish vs. Italian) or different (Spanish vs. Mandarin). On each trial, participants heard two sentences spoken by two individuals, each spoken in an unfamiliar language. The pair was followed by a third sentence spoken in one of the two languages. Participants were asked to judge whether the third sentence was spoken by the first speaker or the second speaker. Across studies, both the difficulty of the discrimination contrast and the relation between exposure and test materials affected children’s performance. In particular, language discrimination performance was facilitated by an initial exposure to a different unfamiliar language, suggesting that experience can help tune children’s attention to the relevant features of novel languages.
Low cost logarithmic techniques for high-precision computations

In this paper, we propose a novel high-precision logarithmic conversion method that relies on linear approximation to reduce the hardware cost and non-linear approximation to increase the conversion precision. It has been shown that for an 8-bit number conversion, the proposed method can achieve a precision of 10 fractional bits with only 24 Look-Up Table (LUT) entries, thereby justifying the approach for incorporation into low-cost and high-precision applications such as an environment modeling strategy for dynamic path planning.
An in vitro comparative evaluation of different intraorifice barriers on the fracture resistance of endodontically treated roots obturated with gutta-percha

Aim: To compare and evaluate the root reinforcement potential of four different intraorifice barriers: Mineral trioxide aggregate (MTA), resin-modified glass ionomer cement (RMGIC), fiber-reinforced composite (FRC), and nanohybrid composite (NC). Materials and Methods: Seventy-five mandibular premolars were decoronated to a standardized length, and prepared and obturated with gutta-percha and AH Plus sealer. Except for control specimens, the coronal 3-mm gutta-percha was removed and filled with different materials. The specimens (75) were divided into five groups (n = 15) on the basis of the intraorifice barrier material used. Group 1: MTA, Group 2: RMGIC, Group 3: FRC, Group 4: NC, Group 5: no barrier (control). Fracture resistance of the specimens was tested. Results: Fracture resistance of roots was significantly affected by the type of intraorifice barrier used and the following pattern was observed: RMGIC > FRC > NC > MTA. Conclusion: Intraorifice barriers can be regarded as a viable choice to reduce the occurrence of postendodontic root fractures. Among the four tested materials, RMGIC showed the maximum reinforcement.
Novel CYP2C9 Promoter Variants and Assessment of Their Impact on Gene Expression

There are a considerable number of reports identifying and characterizing genetic variants within the CYP2C9 coding region. Much less is known about polymorphic promoter sequences that also might contribute to interindividual differences in CYP2C9 expression. To address this problem, approximately 10,000 base pairs of CYP2C9 upstream information were resequenced using 24 DNA samples from the Coriell Polymorphism Discovery Resource. Thirty-one single-nucleotide polymorphisms (SNPs) were identified; nine SNPs were novel, whereas 22 were reported previously. Using both sequencing and multiplex single-base extension, individual SNP frequencies were determined in 193 DNA samples obtained from unrelated, self-reported Hispanic Americans of Mexican descent, and they were compared with similar data obtained from a non-Latino white cohort. Significant interethnic differences were observed in several SNP frequencies, some of which seemed unique to the Hispanic population. Analysis using PHASE 2.1 inferred nine common (>1%) variant haplotypes, two of which included the g.3608C>T (R144C) CYP2C9*2 and two the g.42614A>C (I359L) CYP2C9*3 SNPs. Haplotype variants were introduced into a CYP2C9/luciferase reporter plasmid using site-directed mutagenesis, and the impact of the variants on promoter activity assessed by transient expression in HepG2 cells. Both constitutive and pregnane X receptor-mediated inducible activities were measured. Haplotypes 1B, 3A, and 3B each exhibited a 65% decrease in constitutive promoter activity relative to the reference haplotype. Haplotypes 1D and 3B exhibited a 50% decrease and a 40% increase in induced promoter activity, respectively. These data suggest that genetic variation within CYP2C9 regulatory sequences is likely to contribute to differences in CYP2C9 phenotype both within and among different populations.
Pyrosequencing of BRAF V600E in routine samples of Hairy Cell Leukaemia identifies CD5+ variant Hairy Cell Leukaemia that lacks V600E

Mikkael A. Sekeres Heesun J. Rogers Ramon V. Tiu Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Clinical Pathology, Cleveland Clinic, and Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA. E-mail: tiur@ccf.org