Miracle-dz/UniFAR-FTUs huggingface dataset:
Active Clustering: Robust and Efficient Hierarchical Clustering using Adaptively Selected Similarities

Hierarchical clustering based on pairwise similarities is a common tool used in a broad range of scientific applications. However, in many problems it may be expensive to obtain or compute similarities between the items to be clustered. This paper investigates the hierarchical clustering of N items based on a small subset of pairwise similarities, significantly less than the complete set of N (N − 1)/2 similarities. First, we show that if the intracluster similarities exceed intercluster similarities, then it is possible to correctly determine the hierarchical clustering from as few as 3N log N similarities. We demonstrate this order of magnitude savings in the number of pairwise similarities necessitates sequentially selecting which similarities to obtain in an adaptive fashion, rather than picking them at random. We then propose an active clustering method that is robust to a limited fraction of anomalous similarities, and show how even in the presence of these noisy similarity values we can resolve the hierarchical clustering using only O ( N log 2 N ) pairwise similarities.
Ultrastructural localization of peroxidase in leukocytes of rat bone marrow and blood

The differentiation of leukocytes in the bone marrow and blood of normal adult male rats was studied by electron microscopy and peroxidase cytochemistry. Tissue samples were fixed in glutaraldehyde, or paraformaldehyde‐glutaraldehyde, and incubated in a peroxidase medium containing 3,3′‐diaminobenzidine and H2O2 at pH 7.6. Mature cells of blood were identified, and then the earlier stages of maturation in bone marrow were analyzed. In immature cells of four cell lines, neutrophils, monocytes, basophils, and eosinophils, peroxidase is synthesized and could be demonstrated in the rough endoplasmic reticulum (RER), Golgi complex, and in cytoplasmic granules. Later in maturation, reaction product for peroxidase could not be found in RER or Golgi complex, indicating that peroxidase synthesis had ceased. In two cell lines, neutrophils and monocytes, peroxidase‐negative granules were formed, and the mature cells contained two populations of cytochemically distinct granules. All granules of mature eosinophils were peroxidasepositive. In mature basophils, some granules were clearly peroxidase‐positive; others displayed variable density, making interpretation uncertain. Mast cells were never seen in blood, but were abundant in bone marrow; peroxidase was never found in their granules by either electron microscopic cytochemistry or a variety of light microscopic methods. Hence, these cells differ from basophils, not only in morphology but also in the enzyme content of their granules.
Type VI collagen in extracellular, 100-nm periodic filaments and fibrils: identification by immunoelectron microscopy

Filaments and fibrils that exhibit a 100-nm axial periodicity and occur in the medium and in the deposited extracellular matrix of chicken embryo and human fibroblast cultures have been tentatively identified with type VI collagen on the basis of their similar structural characteristics (Bruns, R. R., 1984, J. Ultrastruct. Res., 89:136-145). Using indirect immunoelectron microscopy and specific monoclonal and polyclonal antibodies, we now report their positive identification with collagen VI and their distribution in fibroblast cultures and in tendon. Primary human foreskin fibroblast cultures, labeled with anti- type VI antibody and studied by fluorescence microscopy, showed a progressive increase in labeling and changes in distribution with time up to 8 d in culture. With immunoelectron microscopy and monoclonal antibodies to human type VI collagen followed by goat anti-mouse IgG coupled to colloidal gold, they showed in thin sections specific 100-nm periodic labeling on extracellular filaments and fibrils: one monoclonal antibody (3C4) attached to the band region and another (4B10) to the interband region of the filaments and fibrils. Rabbit antiserum to type VI collagen also localized on the band region, but the staining was less well defined. Control experiments with antibodies to fibronectin and to procollagen types I and III labeled other filaments and fibrils, but not those with a 100-nm period. Heavy metal- stained fibrils with the same periodic and structural characteristics also have been found in both adult rat tail tendon and embryonic chicken tendon subjected to prolonged incubation in culture medium or treatment with adenosine 5'-triphosphate at pH 4.6. We conclude that the 100-nm periodic filaments and fibrils represent the native aggregate form of type VI collagen. It is likely that banded fibrils of the same periodicity and appearance, reported by many observers over the years in a wide range of normal and pathological tissues, are at least in part, type VI collagen.
The relationship of thermospheric density anomaly with electron temperature, small-scale FAC, and ion up-flow in the cusp region, as observed by CHAMP and DMSP satellites

Abstract. We present in a statistical study a comparison of thermospheric mass density enhancements (ρrel) with electron temperature (Te), small-scale field-aligned currents (SSFACs), and vertical ion velocity (Vz) at high latitudes around noon magnetic local time (MLT). Satellite data from CHAMP (CHAllenging Minisatellite Payload) and DMSP (Defense Meteorological Satellite Program) sampling the Northern Hemisphere during the years 2002–2005 are used. In a first step we investigate the distribution of the measured quantities in a magnetic latitude (MLat) versus MLT frame. All considered variables exhibit prominent peak amplitudes in the cusp region. A superposed epoch analysis was performed to examine causal relationship between the quantities. The occurrence of a thermospheric relative mass density anomaly, ρrel >1.2, in the cusp region is defining an event. The location of the density peak is taken as a reference latitude (Δ MLat = 0°). Interestingly, all the considered quantities, SSFACs, Te, and Vz are co-located with the density anomaly. The amplitudes of the peaks exhibit different characters of seasonal variation. The average relative density enhancement of the more prominent density peaks considered in this study amounts to 1.33 during all seasons. As expected, SSFACs are largest in summer with average amplitudes equal to 2.56 μA m−2, decaying to 2.00 μA m−2 in winter. The event related enhancements of Te and Vz are both largest in winter (Δ Te =730 K, Vz =136 m s−1) and smallest in summer (Δ Te = 377 K, Vz = 57 m s−1. Based on the similarity of the seasonal behaviour we suggest a close relationship between these two quantities. A correlation analysis supports a linear relation with a high coefficient greater than or equal to 0.93, irrespective of season. Our preferred explanation is that dayside reconnection fuels Joule heating of the thermosphere causing air upwelling and at the same time heating of the electron gas that pulls up ions along affected flux tubes.
Metaphase karyotypes and G‐banding in sandflies of the Lutzomyia longipalpis complex

Abstract. Mitotic metaphase chromosomes (2n = 8) from brain cells of fourth instar sandfly larvae of four geographical strains of the Lutzomyia longipaplis complex were examined microscopically, with bright‐field illumination, after staining by a new G‐banding technique involving exposure of air‐dried chromosome preparations to quinacrine and ultraviolet light. Differences of G‐banding and/or position of the centromere on chromosome 4 (the smallest chromosome pair) distinguished four putative sibling species from Costa Rica, Colombia and Brazil (distinctive populations from Jacobina and Lapinha Caves). The karyotype of the population from Jacobina, Brazil, showed an apparently plesiomorphic pattern of G‐banding. On the basis of their recognizably different mitotic karyotypes, cytogenetic identification of separate taxa in the L. longipalpis complex should be useful for specific female vector competence and ecology studies.
Incidence of postoperative symptomatic epidural hematoma in spinal decompression surgery.

OBJECT Neurological deterioration due to spinal epidural hematoma (SEH) is a rare but significant complication of spinal surgery. The frequency of hematoma evacuation after spinal surgery is reportedly 0.1%-3%. The objective of this study was to investigate the symptomatology of SEH and the frequency of evacuation for each surgical procedure after spinal decompression surgery. METHODS This is a retrospective study of 26 patients who underwent SEH evacuation after spinal decompression surgery between 1986 and 2005. During this period, 6356 spinal decompression surgeries were performed. The factors studied were the frequency of SEH evacuation for each surgical procedure, symptoms, time to SEH evacuation, comorbidities, and neurological recovery. RESULTS The frequency of SEH evacuation was 0.41% (26 of 6356) for all operations. The frequency for each surgical procedure was 0% (0 of 1568) in standard lumbar discectomy, 0.50% (8 of 1614) in lumbar laminectomy, 0.67% (8 of 1191) in posterior lumbar interbody fusion, 4.46% (5 of 112) in thoracic laminectomy, 0.44% (4 of 910) in cervical laminoplasty, and 0.21% (1 of 466) in cervical anterior spinal fusion. Nine patients had comorbidities involving hemorrhage. Spinal epidural hematoma evacuation was performed between 4 hours and 8 days after the initial operation. Whereas severe paralysis was observed within 24 hours in most patients undergoing cervical and/or thoracic surgery, half of the patients undergoing lumbar surgery had symptoms of SEH such as leg pain or bladder dysfunction after suction drain removal. The shorter the period to evacuation, the better were the results of neurological recovery. CONCLUSIONS Postoperative SEH was most frequent after thoracic laminectomy. In cervical and thoracic surgeries, symptoms of SEH were noted within 24 hours, mostly severe paralysis, and almost half of the lumbar surgery patients had symptoms after suction drain removal.
Localization of Erythrocyte Membrane Sulfhydryl Groups Essential for Glucose Transport

The reactions of three organic mercurial compounds, chlormerodrin, parachloromercuribenzoate (PCMB), and parachloromercuribenzenesulfonate (PCMBS) with intact red blood cells, hemolyzed red cells, hemoglobin solutions, and hemoglobin-free ghosts have been characterized. Both PCMB and PCMBS react with only 2 to 3 sulfhydryl groups per mole of hemoglobin in solution, whereas chlormerodrin reacts with 6 to 7. In hemoglobin-free ghosts, however, all three reagents react with a similar number of sulfhydryl groups, approximately 4 x 10-17 moles per cell, or about 25 per cent of the total stromal sulfhydryl groups, which react with inorganic mercuric chloride. In the intact cell the membrane imposes a diffusion barrier; chlormerodrin and PCMB penetrate slowly, whereas PCMBS does not. Kinetic studies of chlormerodrin binding to intact cells reveal that the majority of stromal sulfhydryl groups is located inside the diffusion barrier, with only 1 to 1.5 per cent (or 1 to 1,400,000 sites per cell) located outside of this barrier. Reaction of PCMBS with intact cells is limited to this small fraction on the outer membrane surface. All three reagents are capable of inhibiting glucose transport in the red cell. With chlormerodrin and PCMBS it was demonstrated that the inhibition results from interactions with the sulfhydryl groups located on the outer surface of the membrane.
Two-stage reimplantation of infected hip arthroplasties.

BACKGROUND Although two-stage reimplantation for infected hip arthroplasty has a high success rate, the protocols of the antibiotic therapy after resection arthroplasty have varied in different reports. The purpose of this study was to evaluate the clinical outcomes of two-stage reimplantation for infected hip arthroplasty using our protocol of combined parenteral and oral antibiotic therapy and the criterion for reimplantation. METHODS Forty-seven patients (48 hips) with infected hip arthroplasty were treated with two-stage reimplantation using interim antibiotic-impregnated cement beads with an average 2.6 weeks of parenteral antibiotic and 6 weeks of oral antibiotic therapy. The timing for reimplantation was determined using the values of erythrocyte-sedimentation rate (ESR) and C-reactive protein (CRP) with no clinical signs of infection. The average follow-up period was 5.6 years. RESULTS Forty-six (96%) hips were free of recurrent infection according to clinical examination and laboratory tests at the latest follow up. All 48 hips had negative tissue culture results obtained at the second-stage reimplantation except one which resulted in a recurrent infection. The average interim period of time from the first-stage procedure to reimplantation was 5.4 months (range, 2-24 months). Two hips had recurrent infections after reimplantation. The mean Harris hip score improved from 26 points preoperatively to 83 points at the latest follow up. Thirty-five patients (74%) achieved excellent or good results. CONCLUSIONS Two-stage reimplantation of an infected hip arthroplasty can achieve a high success rate using the protocol of aggressive surgical debridement, local antibiotic-loaded cement beads, combined parenteral and oral antibiotic therapy and reimplantation after normalization of ESR and CRP levels.
Network Stability from Activity-Dependent Regulation of Neuronal Conductances

Activity-dependent plasticity appears to play an important role in the modification of neurons and neural circuits that occurs during development and learning. Plasticity is also essential for the maintenance of stable patterns of activity in the face of variable environmental and internal conditions. Previous theoretical and experimental results suggest that neurons stabilize their activity by altering the number or characteristics of ion channels to regulate their intrinsic electrical properties. We present both experimental and modeling evidence to show that activity-dependent regulation of conductances, operating at the level of individual neurons, can also stabilize network activity. These results indicate that the stomatogastric ganglion of the crab can generate a characteristic rhythmic pattern of activity in two fundamentally different modes of operation. In one mode, the rhythm is strictly conditional on the presence of neuromodulatory afferents from adjacent ganglia. In the other, it is independent of neuromodulatory input but relies on newly developed intrinsic properties of the component neurons.
High Salt Intake Down-Regulates Colonic Mineralocorticoid Receptors, Epithelial Sodium Channels and 11β-Hydroxysteroid Dehydrogenase Type 2

Besides the kidneys, the gastrointestinal tract is the principal organ responsible for sodium homeostasis. For sodium transport across the cell membranes the epithelial sodium channel (ENaC) is of pivotal relevance. The ENaC is mainly regulated by mineralocorticoid receptor mediated actions. The MR activation by endogenous 11β-hydroxy-glucocorticoids is modulated by the 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2). Here we present evidence for intestinal segment specific 11β-HSD2 expression and hypothesize that a high salt intake and/or uninephrectomy (UNX) affects colonic 11β-HSD2, MR and ENaC expression. The 11β-HSD2 activity was measured by means of 3H-corticosterone conversion into 3H-11-dehydrocorticosterone in Sprague Dawley rats on a normal and high salt diet. The activity increased steadily from the ileum to the distal colon by a factor of about 3, an observation in line with the relevance of the distal colon for sodium handling. High salt intake diminished mRNA and protein of 11β-HSD2 by about 50% (p<0.001) and reduced the expression of the MR (p<0.01). The functionally relevant ENaC-β and ENaC-γ expression, a measure of mineralocorticoid action, diminished by more than 50% by high salt intake (p<0.001). The observed changes were present in rats with and without UNX. Thus, colonic epithelial cells appear to contribute to the protective armamentarium of the mammalian body against salt overload, a mechanism not modulated by UNX.
Microstructural and properties evaluation of M2 high speed steel after inoculating addition of powder W and WC

Abstract Melt treatment methods that involve the addition of small amounts of surface-active or/and inoculating elements have permitted the development of improved high speed steels (HSSs) with greater carbide control. In this work, addition of powdered W and WC into the melt was used to improve the as cast microstructure of AISI M2 HSS and, as consequence, its properties after full heat treatment. Under the action of inoculants, there was a refinement of the primary grains of the matrix and a transition from a columnar dendritic mode of solidification (typically found in uninoculated AISI M2) to a predominantly equiaxed morphology in the inoculated steels. SEM and EDS confirmed that the inoculation favoured the formation of the M6C eutectic at the expense of the M2C and MC variants, which prevailed in the as cast microstructure of the uninoculated steel. The relationship between microstructure and the properties is discussed.
GOAL: automated Gene Ontology analysis of expression profiles

One of the most common problems encountered while deciphering results from expression profiling experiments is in relating differential expression of genes to molecular functions and cellular processes. A second important problem is that of comparing experiments performed by different labs using different microarray platforms, or even unrelated techniques. Gene Ontology (GO) is now used to describe biological features, since GO terms are associated with genes, to overcome the apparent distance between expression profiles and biological comprehension. Here we describe the development, implementation and use of GOAL (Gene Ontology Automated Lexicon), a web-based application for the identification of functions and processes regulated in microarray and SAGE (serial analysis of gene expression) experiments. We applied GOAL to a range of experimental datasets related to different biological problems, including cancer and the cell cycle. By using GOAL, reported and novel relevant processes were identified in a number of experiments by our collaborators and by us. Different datasets could also be compared with each other to define conserved functional modules. GOAL allows a seamless and high-level analysis of expression profiles and is implemented as a free WWW resource (http://microarrays.unife.it).
Targeting the Wolbachia Cell Division Protein FtsZ as a New Approach for Antifilarial Therapy

The use of antibiotics targeting the obligate bacterial endosymbiont Wolbachia of filarial parasites has been validated as an approach for controlling filarial infection in animals and humans. Availability of genomic sequences for the Wolbachia (wBm) present in the human filarial parasite Brugia malayi has enabled genome-wide searching for new potential drug targets. In the present study, we investigated the cell division machinery of wBm and determined that it possesses the essential cell division gene ftsZ which was expressed in all developmental stages of B. malayi examined. FtsZ is a GTPase thereby making the protein an attractive Wolbachia drug target. We described the molecular characterization and catalytic properties of Wolbachia FtsZ. We also demonstrated that the GTPase activity was inhibited by the natural product, berberine, and small molecule inhibitors identified from a high-throughput screen. Furthermore, berberine was also effective in reducing motility and reproduction in B. malayi parasites in vitro. Our results should facilitate the discovery of selective inhibitors of FtsZ as a novel anti-symbiotic approach for controlling filarial infection. Note The nucleotide sequences reported in this paper are available in GenBank™ Data Bank under the accession number wAlB-FtsZ (JN616286).
Is Morality Unified? Evidence that Distinct Neural Systems Underlie Moral Judgments of Harm, Dishonesty, and Disgust

Much recent research has sought to uncover the neural basis of moral judgment. However, it has remained unclear whether “moral judgments” are sufficiently homogenous to be studied scientifically as a unified category. We tested this assumption by using fMRI to examine the neural correlates of moral judgments within three moral areas: (physical) harm, dishonesty, and (sexual) disgust. We found that the judgment of moral wrongness was subserved by distinct neural systems for each of the different moral areas and that these differences were much more robust than differences in wrongness judgments within a moral area. Dishonest, disgusting, and harmful moral transgression recruited networks of brain regions associated with mentalizing, affective processing, and action understanding, respectively. Dorsal medial pFC was the only region activated by all scenarios judged to be morally wrong in comparison with neutral scenarios. However, this region was also activated by dishonest and harmful scenarios judged not to be morally wrong, suggestive of a domain-general role that is neither peculiar to nor predictive of moral decisions. These results suggest that moral judgment is not a wholly unified faculty in the human brain, but rather, instantiated in dissociable neural systems that are engaged differentially depending on the type of transgression being judged.
Levels of carcinoembryonic antigen and CA 19-9 in the sera and peritoneal washing of patients undergoing surgical treatment for gastric carcinoma.

BACKGROUND Early peritoneal recurrence of gastric carcinoma following curative resection remains a great challenge in the treatment and prevention of this disease. AIM To analyze the relationship between levels of tumor markers, carcinoembryonic antigen (CEA) and CA 19-9 in the sera and peritoneal washing, and anatomopathological aspects of the gastric carcinoma. METHODS Of the 46 patients in the study, 29 (63.0%) were males and 17 (37.0%) females. Mean age was 63.6 +/- 11.7 years (31 to 91 years). Peripheral venous blood samples were collected from the upper limb vein from both patient groups after anesthetic induction, in order to determine serum levels of CEA and CA 19-9. After the end of the procedure, 50 mL of physiologic solution was introduced into the bottom of the Douglas sack and a portion aspirated to determine CEA and CA 19-9 levels in the peritoneal washing. Levels of CEA and CA 19-9 in the sera and peritoneal washing were compared to the following variables: lesion diameter < or = 4 cm or > 4 cm, lymph node involvement, angiolymphatic invasion, depth of invasion into gastric wall, and initial or late stage. RESULTS Sera CEA levels were significantly higher in patients with lesions >5 cm. CEA levels in the sera and peritoneal washing were significantly greater in patients with signet ring cell gastric carcinoma. In addition, levels of CEA in peripheral blood and peritoneal washing showed significant association with the degree of carcinoma penetration into the gastric wall, while sera CEA was significantly higher in patients at more advanced stages. There was no significant difference between sera and peritoneal CEA values regarding grade of differentiation. Patients with gastric lesions measuring > 5 cm and more differentiated lesions had significantly higher sera CA 19-9 values. In patients with lymph nodes invasion by gastric carcinoma, CA 19-9 levels in peritoneal washing were significantly higher than in peripheral blood. Levels of CA 19-9 in peritoneal washing were significantly greater at advanced stages than the initial stage of the gastric carcinoma. CONCLUSIONS Elevated levels of CA 19-9 in peritoneal washing were significantly associated with more advance stages of gastric carcinoma and was more reliable predictive factor for staging than sera CA 19-9 levels. CEA levels in the sera more accurately reflected neoplasia stage than levels in peritoneal washing.