Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Trypanosoma evansi in camel abortions (Camelus dromedarius) in Iran using polymerase chain reaction

Trypanosoma evansi is a blood parasite protozoan that causes trypanosomiasis or surra in a variety of economically valued animals such as cattle and camels. This infection causes abortion in camels. The present study was conducted to evaluate the presence of Trypanosoma evansi in aborted fetuses of Iranian camels Camelus dromedarius by polymerase chain reaction PCR method. In this study, 244 abomasal contents of aborted fetuses were collected from an Iranian camel herd in the east of Iran. The results showed that 41 of 244 16.8% aborted fetuses were infected with Trypanosoma evansi DNA. The results showed that a high percentage of abortions in Iranian camel herds were due to Trypanosoma evansi infection. There was a significant difference in positive Trypanosoma evansi DNA in aborted fetuses between sampling locations P < 0.05 .
Measuring the competitive trends of the South African citrus industry

This paper analyses the competitive trends of the South African citrus industry, making use of the relative trade advantage model to calculate such competitive trends over time. The data to measure competitive performance was obtained from the Food and Agricultural Organization and the International Trade Centre. Results reveal that the industry is competitive and has maintained positive figures since the early 1960s. Results also indicate that, when compared with global competitors, it is being challenged by the most powerful nations in both southern and northern hemispheres, and this indicates the need for the industry to develop meaningful strategies that can enhance the its competitive performance.
Constructive analysis, types and exact real numbers

In this paper we will discuss various aspects of computable/constructive analysis, namely semantics, proofs and computations. We will present some of the problems and solutions of exact real arithmetic varying from concrete implementations, representation and algorithms to various models for real computation. We then put these models in a uniform framework using realisability, which opens the door to the use of type theoretic and coalgebraic constructions both in computing and reasoning about these computations. We will indicate that it is often natural to use constructive logic to reason about these computations.
Pricing via Functional Size - A Case Study of a Company's Portfolio of 77 Outsourced Projects

A medium-sized west-European telecom company experienced a worsening trend in performance, indicating that the organization did not learn from history, in combination with much time and energy spent on preparation and review of project proposals. In order to create more transparency in the supplier proposal process a pilot was started on Functional Size Measurement pricing (FSM-pricing). In this paper we evaluate the implementation of FSM-pricing in the software engineering domain of the company, as an instrument useful in the context of software management and supplier proposal pricing. We analyzed 77 finalized software engineering projects, covering 14 million Euro project cost and a project portfolio size of more than 5,000 function points. We found that a statistical, evidence-based pricing approach for software engineering, as a single instrument (without a connection with expert judgment), can be used in the subject companies to create cost transparency and performance management of software project portfolios.
Globular and disordered—the non-identical twins in protein-protein interactions

In biology proteins from different structural classes interact across and within classes in ways that are optimized to achieve balanced functional outputs. The interactions between intrinsically disordered proteins (IDPs) and other proteins rely on changes in flexibility and this is seen as a strong determinant for their function. This has fostered the notion that IDP's bind with low affinity but high specificity. Here we have analyzed available detailed thermodynamic data for protein-protein interactions to put to the test if the thermodynamic profiles of IDP interactions differ from those of other protein-protein interactions. We find that ordered proteins and the disordered ones act as non-identical twins operating by similar principles but where the disordered proteins complexes are on average less stable by 2.5 kcal mol−1.
Generalized Belief Propagation on Tree Robust Structured Region Graphs

This paper provides some new guidance in the construction of region graphs for Generalized Belief Propagation (GBP). We connect the problem of choosing the outer regions of a Loop-Structured Region Graph (SRG) to that of finding a fundamental cycle basis of the corresponding Markov network. We also define a new class of tree-robust Loop-SRG for which GBP on any induced (spanning) tree of the Markov network, obtained by setting to zero the off-tree interactions, is exact. This class of SRG is then mapped to an equivalent class of tree-robust cycle bases on the Markov network. We show that a tree-robust cycle basis can be identified by proving that for every subset of cycles, the graph obtained from the edges that participate in a single cycle only, is multiply connected. Using this we identify two classes of tree-robust cycle bases: planar cycle bases and "star" cycle bases. In experiments we show that tree-robustness can be successfully exploited as a design principle to improve the accuracy and convergence of GBP.
A MODEL FOR IMMUNOLOGICAL MATURATION BASED ON TEE CONVERSION OF HAPTENS TO CARRIERS BY ANTIBODY* BY RAYMOND A. McBRIDE,;~ M.D., Am~ LOUIS W. SCHIERMAN, PzI.D

Recognition of immunogenicity is thought to be mediated by specific receptor antibody molecules which are either freely circulating or bound to cell membranes (1-5). In conventional hapten-carrier systems an essential requirement for activation of antihapten antibody synthesis is the ability of the immune system to recognize the immunogenicity of the carrier; induction of immunological tolerance to the carrier results in reduced anticarrier and antihapten antibody synthesis following subsequent inoculation of the hapten-carrier complex (6-8). Furthermore, a secondary type immune response to a hapten is most easily achieved if the same carrier is employed in both primary and secondary stimuli; little or no response results if the carrier for the secondary stimulus differs from the carrier used for activation of the primary immune response (2). Since procedures which activate specific anticarrier antibody formation [preimmunization with carrier (2, 7) or transfer of cells containing anticarrier antibody (9)] enhance the synthesis of antihapten antibodies, it is likely that the specific carrier effect on the immunogenicity of hapten is mediated in part by anticarrier antibedy. Experiments in which anticarrier antibody v~as injected prior to the synthetic hapten-carrier complex have not demonstrated an enhancement of antihapten antibody synthesis (2, 7, 9). These results have been interpreted as indicating that the relevant receptors are not present in the serum. In chickens, isoantigens determined by the B blood group locus behave as carriers for isoantigens determined by the A blood group locus (10). In the isoantigen system, as with conventional hapten-carrier complexes, recognition of the immunogenicity of the carrier is necessary for an immune response to the hapten (10). The finding that the carrier effect is enhanced by circulating anticarrier antibody (11, 12) is evidence for an important role of carrier antibody in the activation of an antihapten immune response. Pincus and Nussenzweig (13) demonstrated, by means of passive antibody, suppression of the immune response to a portion of guinea pig ~, 2-globulin and simultaneous enhancement of the response to antigenic determinants on another portion of the same molecule. Others have demonstrated an enhancement of the immune response to complex cellular antigens by means of passive antibody (14-17).
THE ABSENCE OF LYSOSOMAL FUSION WITH PHAGOCYTIC VACUOLES CONTAINING LIVING PARASITES*

In the past 15 yr there have been many advances in our knowledge of the intracellular events that follow phagocytosis of microorganisms (1, 2). Lysosomal constituents and metabolic products are delivered to the phagocytic vacuole, and in most instances there ensues rapid death and destruction of the microorganisms. However, certain bacteria or protozoans are clearly capable of surviving inside of cells, and in some instances, toxoplasma being an example, the parasites apparently are able to multiply only in an intracellular environment. Very few studies have been made on the mechanisms by which some parasites can evade or withstand the metabolic factors and hydrolases that usually kill microorganisms in the phagolysosomes of cells. Several different mechanisms might be responsible for parasite survival intracellularly. Some viruses may interact with the plasma membrane or with the vacuolar membrane so that the viral cores reach the host cell cytoplasm without encountering lysosomal and other factors that attack foreign materials in the vacuolar system (3). In some instances microorganisms may be able to prevent the transfer of lysosomal materials to phagocytic vacuoles. Recent experiments indicate that such a mechanism may operate in macrophages infected with tubercle bacilli (4) or with Chlamydia species in fibroblasts (5). Finally, certain parasites may be capable of withstanding the toxic substances and digestive enzymes delivered to the phagocytic vacuoles. Mycobacterium lepraemuriurn apparently is able to survive such exposure (6, 7).
Agglu t in in wi th Sialic Acid Residues on E p i m a s t i g o t e Cells

Chagas's disease is a chronic, debilitating, incurable disease affecting at least 12 million people in Central and South America (1, 2). TTypanosoma cruzi, the etiological agent, exists in three morphologically distinct forms related to different environments where it lives (1, 3): the amastigotes, which represent the multiplying stage found within the cells of mammal ian hosts; the trypomastigotes, which are present in the bloodstream and in infected tissues of mammal ian hosts, in the lumen of the rectum of the transmitting triatomid insect, and in culture; and the third form, epimastigotes, which are found intracellularly in mammal ian hosts as a multiplying form in the vector's digestive tract, and in culture. Although bloodstream, insect, and culture trypomastigotes are highly infective, culture epimastigotes have very little, if any, capacity to initiate infection in the mammal ian host (3). Although the morphologically defined forms of T. cruzi perform different functions in the life cycle of the parasite, the molecular mechanisms underlying the distinct behaviors remain unknown. The majority of exposed plasma membrane proteins are glycoproteins (4, 5), and there is increasing evidence that glycoproteins are of major importance in the maturat ion and regulation of functions displayed by cells such as those of the immune system (6, 7). On the other hand, much of the work concerning structure and function of cell surface carbohydrates is derived from studies with lectins, a class of sugarbinding proteins of nonimmune origin (8-10). In our study a systematic analysis of cell surface glyeoproteins and /or of glycolipids of T. cruzi developmental stages was undertaken, using ~30 highly purified, glycosidase-free lectins of various carbohydrate specificities as probes. The results showed that some lectins display unique selectivity in interacting with trypanosome forms as determined by agglutination and binding assays. It also showed that trypomastigotes obtained from blood of infected mice and from culture differed in their surface carbohydrates. Moreover, sialic acid residues detected and quantitated in epimasti-
Biome reconstruction from pollen and plant macrofossil data for Africa and the Arabian peninsula at 0 and 6000 years

Biome reconstruction from pollen and plant macrofossil data provides an objective method to reconstruct past vegetation. Biomes for Africa and the Arabian peninsula have been mapped for 6000 years bp and provide a new standard for the evaluation of simulated palaeovegetation distributions. A test using modern pollen data shows the robustness of the biomization method, which is able to predict the major vegetation types with a high confidence level. The application of the procedure to the 6000 years data set (pollen and plant macrofossil analyses) shows systematic differences from the present that are consistent with the numerous previous regional and continental interpretations, while providing a more extensive and more objective basis for such interpretations. Madagascar, eastern, southern and central Africa show only minor changes in terms of biomes, compared to present. Major changes in biome distributions occur north of 15°N, with steppe in many low‐elevation sites that are now desert, and temperate xerophytic woods/scrub and warm mixed forest in the Saharan mountains. These shifts in biome distributions imply significant changes in climate, especially precipitation, between 6000 years and present, reflecting a change in monsoon extent combined with a southward expansion of Mediterranean influence.
High-precision camera distortion measurements with a "calibration harp"

This paper addresses the high-precision measurement of the distortion of a digital camera from photographs. Traditionally, this distortion is measured from photographs of a flat pattern that contains aligned elements. Nevertheless, it is nearly impossible to fabricate a very flat pattern and to validate its flatness. This fact limits the attainable measurable precisions. In contrast, it is much easier to obtain physically very precise straight lines by tightly stretching good quality strings on a frame. Taking literally "plumb-line methods," we built a "calibration harp" instead of the classic flat patterns to obtain a high-precision measurement tool, demonstrably reaching 2/100 pixel precisions. The harp is complemented with the algorithms computing automatically from harp photographs two different and complementary lens distortion measurements. The precision of the method is evaluated on images corrected by state-of-the-art distortion correction algorithms, and by popular software. Three applications are shown: first an objective and reliable measurement of the result of any distortion correction. Second, the harp permits us to control state-of-the art global camera calibration algorithms: it permits us to select the right distortion model, thus avoiding internal compensation errors inherent to these methods. Third, the method replaces manual procedures in other distortion correction methods, makes them fully automatic, and increases their reliability and precision.
Staphylococcal Enterotoxins, Toxic Shock Syndrome Toxin-I, and Streptococcal Pyrogenic Exotoxins: Some Basic Biology of Bacterial Superantigens

Abstract : Staphylococcus aureus and Streptococcus pyogenes are facultative gram-positive cocci that play an important role in a myriad of human illnesses, including food poisoning, skin infections, pharyngitis, life threatening shock, and autoimmune disorders like arthritis, psoriasis, and atopic dermatitis. These ubiquitous bacteria produce various virulence factors that include superantigens like staphylococcal enterotoxins (SE), toxic shock syndrome toxin-i (TSST-1), and streptococcal pyrogenic exotoxins (SPE). To date, the continually expanding literature describes 15 SE and 6 SPE that differ in amino acid sequence and biological effects (i.e. activation of specific T cells). Picomolar concentrations of these toxins activate specific VB-bearing T cells after binding to major histocompatibility complex class II molecules found on antigen presenting cells. The activated T cells vigorously proliferate with a concomitant production of various proinflammatory cytokines, which in sufficient quantities elicit fever, hypotension, and lethal shock. Various in vitro and in vivo models have been developed to study SE, TSST-1, and SPE, thus providing invaluable tools for understanding how these toxins work and discovering potential vaccines as well as therapeutics. This review summarizes the biological properties of, and potential neutralization strategies for, the SE, TSST-1, and SPE.
Phosphate Buffer Extraction Of Gliosed ALD White Matter

Intermediate (8-9 nm) filaments of human central nervous system astrocytes were isolated from the gliosed white matter of cases of adrenoleukodystrophy (ALD). This hereditary lipidosis is characterized pathologically by demyelination, loss of axons, and replacement of the white matter of the caudal cerebrum by a glial scar. Glial filaments were composed largely of a single protein component with a mol wt of about 49,000 daltons. Smaller components (44,000-39,000 daltons) were detected in some samples, and appear to represent degradation products of the filament protein. Human neurofilaments were isolated from the normal frontal white matter of A L D cases by the standard myelin-free axon technique. Isolated glial and neurofilament proteins comigrated during acrylamide gel electrophoresis in SDS. Polypeptides resulting from cyanogen bromide cleavage of the two filament proteins were the same. Both proteins reacted with rabbit antisera raised against isolated bovine neurofilament protein and human glial fibrillary acidic protein.
Surgical treatment for Xp11.2 translocation renal cell carcinoma with venous thrombus

Abstract The aim of the study was to report the experience and outcomes of Xp11.2 translocation renal cell carcinoma (tRCC) patients with tumor thrombus undergoing radical nephrectomy and thrombectomy. Between January 2017 and December 2017, 66 consecutive patients with RCC and venous thrombus involvement received surgical treatment at Peking University Third Hospital. Of which, 5 patients were confirmed of Xp11.2 tRCC, 61 patients were diagnosed of non-tRCC subtypes including 45 ccRCCs, 10 pRCCs, and 6 other subtypes. Demographic, clinical, operation, pathological and follow-up data were extracted for analysis. Prognostic factors were identified by Cox regression analysis. All the patients received radical nephrectomy and thrombectomy successfully. During a median follow-up of 18 months, 5 patients in non-tRCC group and 1 patient in tRCC group died of disease progression. Survival analysis revealed that Xp11.2 tRCC patients experienced shorter DFS than non-tRCC patients, however, there is no significant difference in OS between two groups. Xp11.2 tRCC histological subtype and presence of metastasis at diagnosis were identified as independent negative factors of DFS by multivariate analysis. Radical nephrectomy with thrombectomy provides an acceptable efficacy for tRCC patients with tumor thrombus extending into the venous system. In addition, multimodality treatment should be considered for advanced Xp11.2 RCCs as this subtype was a negative prognostic factor of DFS.
Fractionation of Activated Reactor Absorption with Zymosan (4 mg/ml) and Precipitation as Euglobulin.--

R e a c t i v e lysls is the consequence of the in te rac t ion of two reagents . One, p rev ious ly called indicator , is a normal s e rum pro te in and has been ident i f ied as C7 (1); the o ther is genera ted b y c o m p l e m e n t ac t iva t ion f rom cer ta in sera (referred to as " r e a c t o r " sera) and has been called a c t i v a t e d reactor . I n this paper the n a t u r e of the ac t i va t ed reac tor is explored and the course of the react ion analyzed.
(From the Mallory Institute of Pathology, DeparOnent of Medical Microbiology, and Channing Laboratory, Boston City Hospital, Boston, Massachusetts 02118; and the Departments of Pathology, and Bacteriology and Immunology, Harvard Medical School Boston, Massachusetts 02118)

Histochemical analysis has indicated the presence of protein (1), lipid (2), and metals (3); and biochemical analysis of isolated granules has revealed the presence of hydrolytic enzymes and a particularly high content of peroxidase (4). The peroxidase has been localized by electron microscopy to the external matrix, rather than the internal crystalloid core (5-8). Insofar as they are subceUular organelles containing hydrolytic enzymes within their limiting membrane, eosinophil granules may be classified as lysosomes (9, 10). Recent studies have shown that the lysosomes of the polymorphonuciear leukocytes are involved in a variety of physiological and pathological events (9, 10). In particular, the granules are intimately associated with the process of phagocytosis (9-14). Electron microscopic studies have established that within minutes after ingestion of a particle, the membranes of the granules fuse with those of the phagocytic vacuoles, and the lysosomal enzymes of the granule gain access to the vacuole (10, 11). In the case of the neutrophil, acid phosphatase (5) and, more recently, peroxidase (15) have been localized by ultrastructural histochemistry within phagocytic vacuoles. Although the phagocytic efficiency of eosinophils is less than that of neutrophils, they are capable of phagocytizing all classes of microorganisms (16), and the phenomena observed in neutrophils occur also in eosinophils. Thus, when the eosinophil granule contacts the ingested particle, it joins its membrane to that of the phagocytic vacuole (10, 11), changes its refractive index (17), and appears to explode (18). Materials of the same electron density as the granule appears within the vacuole (11), and the evidence suggests that the granule's contents, and hence its enzymes, enter the phagocytic vacuole.
Heat Shock Protein 27 Association with the IκB Kinase Complex Regulates Tumor Necrosis Factor α-induced NF-κB Activation*

Heat shock protein 27 (Hsp27) is a ubiquitously expressed member of the heat shock protein family that has been implicated in various biological functions including the response to heat shock, oxidative stress, and cytokine treatment. Previous studies have demonstrated that heat shock proteins are involved in regulating signal transduction pathways including the NF-κB pathway. In this study, we demonstrated that Hsp27 associates with the IκB kinase (IKK) complex and that this interaction was stimulated by tumor necrosis factor α treatment. Phosphorylation of Hsp27 by the kinase mitogen-activated protein kinase-activated protein kinase 2, a downstream substrate of the mitogen-activated protein kinase p38, enhanced the association of Hsp27 with IKKβ to result in decreased IKK activity. Consistent with these observations, treatment of cells with a p38 inhibitor reduced the association of Hsp27 with IKKβ and thus resulted in increased IKK activity. These studies indicate that Hsp27 plays a negative role in down-regulating IKK signaling by reducing its activity following tumor necrosis factor α stimulation.
Durmus Ayan 2_Layout 1

Background: The aim of this study is to examine the relationship among the changes in activities of paraoxonase (PON), arylesterase (ARE) and homocysteine thiolactonase (HTLase) enzyme having antioxidant properties and the development of diabetic nephropathy (DN), one of the most common complications of diabetes. Methods: Normoalbuminuric type-2 diabetic patients (Group II, n=100), microalbuminuric type 2 diabetic patients (Group III, n=100) and the control group (Group I, n=100) were included in the study. The age and gender of the patient groups matched with the age and gender of the control group. HTLase, PON and ARE enzyme activities were measured by the spectrophotometric method using a g-thiobutyrinolactone, paraoxon, and phenylacetate substrates respectively. In this study, an autoanalyzer application was developed in order to measure HTLase enzyme activity for the first time. Results: Serum HTLase, ARE and PON activities of Group III and Group II were significantly low compared to HTLase, ARE and PON results of Group I (p<0.05). Conclusions: Based on our results, PON, ARE and HTLase enzyme activities were found to be decreased due to the increase in the degree of DN.