Miracle-dz/UniFAR-FTUs huggingface dataset:
The Classification of the Colon-Aerogenes Group of Bacteria in Relation to their Habitat and its Application to the Sanitary Examination of Water Supplies in the Tropics and in Temperate Climates. A Comparative Study of 2500 Cultures

(1) The ”lactose+ indol+” index as employed in temperate climate is usually an adequate criterion of water purity. (2) Where a positive test does not appear to be substantiated by the sanitary findings, a further differentiation of the organisms isolated becomes necessary. The methyl-red and citrate tests have been found to supply that differentiation in a satisfactory manner. (3) In the Tropics, false positive “lactose-indol” tests are commonly encountered, owing to the presence in large numbers in soil and water of organisms derived from sources other than recently excreted faeces. (4) In the Tropics, the lactose-indol test should always be confirmed by the methyl-red, citrate and saccharose tests or such other reactions or groups of reactions as may be found by a local survey to be applicable. My very grateful thanks are due to Dr P. A. Clearkin, Deputy Director of Laboratory Service, Tanganyika Territory, for his ready advice and constant encouragement; and also to Mr W. Whitley, Analytical Chemist, who performed a chemical analysis of the water samples, and very kindly gave me the benefit of his opinion on them. In addition I have to thank Dr R. R. Scott, Medical Officer of Health, and the Staff of the Health Office, Dar-es-Salaam, who have rendered every facility in the choice and collection of samples. It is a pleasure to be able to record once more my indebtedness to Prof. Bigger, of Trinity College, Dublin, whose fund of valuable suggestions and kindly criticism has been ever at my disposal.
CzcP is a novel efflux system contributing to transition metal resistance in Cupriavidus metallidurans CH34

Cupriavidus metallidurans CH34 possesses a multitude of metal efflux systems. Here, the function of the novel PIB4‐type ATPase CzcP is characterized, which belongs to the plasmid pMOL30‐mediated cobalt‐zinc‐cadmium (Czc) resistance system. Contribution of CzcP to transition metal resistance in C. metallidurans was compared with that of three PIB2‐type ATPases (CadA, ZntA, PrbA) and to other efflux proteins by construction and characterization of multiple deletion mutants. These data also yielded additional evidence for an export of metal cations from the periplasm to the outside of the cell rather than from the cytoplasm to the outside. Moreover, metal‐sensitive Escherichia coli strains were functionally substituted in trans with CzcP and the three PIB2‐type ATPases. Metal transport kinetics performed with inside‐out vesicles identified the main substrates for these four exporters, the Km values and apparent turn‐over numbers. In combination with the mutant data, transport kinetics indicated that CzcP functions as ‘resistance enhancer’: this PIB4‐type ATPase exports transition metals Zn2+, Cd2+ and Co2+ much more rapidly than the three PIB2‐type proteins. However, a basic resistance level has to be provided by the PIB2‐type efflux pumps because CzcP may not be able to reach all different speciations of these metals in the cytoplasm.
Algorithms for Packing and Scheduling Second Year Progress Report Student :

This is the Second Year Progress Report for the “Algorithms for Packing and Scheduling” Ph.D. project. In this report, we give the aims of the project, a summary of the current results obtained, we address the questions raised in the Postgraduate Workshop, and we conclude with possible future work and a timetabled research plan. The project is concerned with the study, design, and analysis, of deterministic online and offline algorithms. We present the current results obtained for packing and scheduling algorithms. More specifically, for the online dynamic bin packing problem we first present a new lower bound of 8/3 ∼ 2.666 for the one-dimensional model. Secondly, we give algorithms for the twoand three-dimensional model when the input consists of unit fraction (lengths are 1 k , for some integer k ≥ 1) and power fraction (lengths are 1 2k , for some integer k ≥ 0) items. For scheduling algorithms, we present a polynomial time optimal offline algorithm for minimizing the electricity cost in Smart Grid. We consider the model in which the power requirement and the duration a request needs service are both unit-size. A possible future direction is to consider a generalization of this model. 1 Aims of the project This project is concerned with the study of algorithms for packing and scheduling. The aims of the project are the study of existing algorithms for packing and scheduling problems, design and analysis of improved algorithms for these problems, formulation of new problems for scheduling, and possibly experimental studies for some of the problems. In particular, for packing problems we look at the online dynamic bin packing problem, while for scheduling problems we consider an offline problem where we aim to minimize the total electricity cost in Smart Grid. 2 Summary of results In this section, we introduce the two types of problems we consider, for online packing algorithms and for an offline scheduling algorithm. For both types, we give an introduction to the problem and summarize the results obtained.
Sputum conversion among patients with pulmonary tuberculosis: are there implications for removal of respiratory isolation?

BACKGROUND Limited data are available to predict the length of time required for a patient to achieve sputum culture conversion after starting therapy for pulmonary tuberculosis. METHODS Rates of sputum smear and culture conversion were determined at weeks 2, 4, 8 and 16 after initiating therapy in patients admitted to our Respiratory Isolation Unit from January 1997 to December 2003. RESULTS For the 184 patients included in the analysis, the mean time from the initiation of appropriate therapy to sputum culture and smear conversion were 34 +/- 26 and 38 +/- 32 days (mean +/- SD) respectively. Only 53% of patients obtained negative sputum cultures within the first 4 weeks of therapy. Multivariate analysis showed that the persistence of positive cultures during the first 4 weeks of therapy was associated with high bacillary counts in sputum smears at diagnosis [OR: 2.86; 95% confidence interval (95% CI): 1.20-6.66], lung cavitations (OR: 4.0; 95% CI: 1.63-9.09) and a prolonged period of symptoms (OR: 3.57; 95% CI: 1.43-3.57). The only factor associated with the persistence of positive cultures after more than 16 weeks of therapy was infection with a multidrug-resistant strain. CONCLUSIONS High initial sputum bacillary counts and drug resistance result in delayed culture conversion. This should be taken into account when decisions regarding the potential discontinuation of isolation are made. The early identification of drug resistance is important for effective infection control in hospitals.
Presupposition: What went wrong?

When the first generation of generative linguists discovered presuppositions in the late 1960s and early 1970s, the initial set of examples was quite small. Aspectual verbs like stop were discussed already by Greek philosophers, proper names, Kepler , and definite descriptions, the present king of France , go back to Gottlob Frege and Bertrand Russell by the turn of the century. Just in the span of a few years my generation of semanticists assembled a veritable zoo of ‘presupposition triggers’ under the assumption that they were all of the same species. Generations of students have learned about presuppositions from Stephen Levinson’s 1983 book on Pragmatics that contains a list of 13 types of presupposition triggers, an excerpt of an even longer unpublished list attributed to a certain Lauri Karttunen. My task in this presentation is to come clean and show why the items on Levinson’s list should not have been lumped together. In retrospect it is strange that the early writings about presupposition by linguists and even by philosophers like Robert Stalnaker or Scott Soames do not make any reference to the rich palette of semantic relations they could have learned from Frege and later from Paul Grice. If we had known Frege’s concepts of Andeutung – Grice’s conventional implicature – and Nebengedanke, it would have been easy to see that there are types of author commitment that are neither entailments nor presuppositions.
Localized mediastinal lymph‐node hyperplasia resembling thymoma

N the course of studying tumors of the I thymus gland we came across a small group of cases in which enlarged mediastinal lymph nodes resembled thymic tumors grossly, radiologically, and even microscopically; and they had been so classified. We wish to report a series of thirteen cases from the Massachusetts General Hospital, the Armed Forces Institute of Pathology, and the University of Havana, as well as individual cases from various pathologists. Case l has previously been reported in the Case Records of the Massachusetts General Hospita1;z cases 9 and 13 were included in a paper given by one of us (L.I.) before the American Association of Pathologists and Bacteriologists5 and a brief description of the condition was included in the fascicle on Tumors of the Thymus Gland.1 Cases 5 and 10 have been reported as thymomass, (we believe erroneously). Clinically most of these patients had no symptoms, the mediastinal shadow being discovered on a routine chest roentgenogram (Figs. 1,A; 2,A; 3; 4; 5,A). A few of the patients consulted their physician because of frequent colds and cough. There was no history of weakness or symptoms suggesting myasthenia gravis. There was no sex predominance and their ages ranged from 19 to 54 years. T h e benign character of the lesion is attested to by the fact that some had been present without change in size (radiologically) for as long as eight years and that there have been no recurrences locally nor any evidence of other lesions elsewhere after removal of the mass. At operation only two of the masses were located in the mid-superior anterior medias-
Detection of herpesvirus DNA in the large intestine of patients with ulcerative colitis and Crohn's disease using the nested polymerase chain reaction

The prevalence of herpesvirus DNA was examined in inflammatory bowel disease tissue. DNA was extracted from resection and biopsy specimens of the large intestine from patients with ulcerative colitis (n = 21), patients with Crohn's disease (n = 29), and patients with noninflammatory bowel disease (controls) (n = 21). The nested polymerase chain reaction was used to detect viral DNA using primer pairs specific for either cytomegalovirus (CMV), herpes simplex virus 1 (HSV1), human herpesvirus 6 (HHVG), varicella zoster virus (VZV), or Epstein Barr virus (EBV). HSV1 and VZV DNA were not detected in any of the tissue samples. There was a high prevalence of CMV (81%), HHVG (76%), and EBV (76%) DNA in ulcerative colitis tissue compared to Crohn's disease tissues (CMV 66%, HHVG 45%, EBV 55%). Control tissue had a relatively low frequency of CMV (29%) and EBV (19%) DNA but a prevalence of HHVG DNA similar to that of ulcerative colitis (86%). However, the simultaneous presence of HHVG and CMV and/or EBV DNA in ulcerative colitis tissue (76%) was much greater than in either Crohn's disease tissues (38%) or control tissue (29%) (P < 0.05). There was a low prevalence of CMV, HHV6, and EBV DNA in peripheral blood mononuclear cells from all patient groups. CMV and EBV are capable of reactivating HHV6: the high prevalence of coexistent HHV6 infection with either or both of these two viruses in ulcerative colitis tissue suggests that they may play a synergistic role in the pathogenesis of this disease. © 1992 Wiley‐Liss, Inc.
Family quality of life: a qualitative inquiry.

In this qualitative inquiry we investigated the conceptualization of family quality of life. Focus groups and individual interviews were conducted with 187 individuals: family members (e.g., parents, siblings) of children with a disability, individuals with a disability, family of children without a disability, service providers, and administrators. Data were collected in urban and rural settings to elicit the participants' understanding of family quality of life. Ten domains of family quality of life were identified and described in terms of subdomains, indicators, and key points raised by participants. Implications are discussed in terms of future directions for research and family support.
Ensemble Coding of Vocal Control in Birdsong

Zebra finch song is represented in the high-level motor control nucleus high vocal center (HVC) (Reiner et al., 2004) as a sparse sequence of spike bursts. In contrast, the vocal organ is driven continuously by smoothly varying muscle control signals. To investigate how the sparse HVC code is transformed into continuous vocal patterns, we recorded in the singing zebra finch from populations of neurons in the robust nucleus of arcopallium (RA), a premotor area intermediate between HVC and the motor neurons. We found that highly similar song elements are typically produced by different RA ensembles. Furthermore, although the song is modulated on a wide range of time scales (10-100 ms), patterns of neural activity in RA change only on a short time scale (5-10 ms). We suggest that song is driven by a dynamic circuit that operates on a single underlying clock, and that the large convergence of RA neurons to vocal control muscles results in a many-to-one mapping of RA activity to song structure. This permits rapidly changing RA ensembles to drive both fast and slow acoustic modulations, thereby transforming the sparse HVC code into a continuous vocal pattern.
Detailed characterization and critical discussion of series resistance in graphene-metal contacts

We apply the contact-end resistance method to TLM structures in order to characterize the graphene-metal contact resistance. A critical analysis of the experimental results shows that the commonly used transmission line model fails to accurately describe the graphene-metal contact under specific biasing conditions. The experiments suggest the presence of an additional resistance contribution associated to the p-p+ junction induced in the graphene in the proximity of the contact. This voltage dependent resistance limits the range of applicability of the extraction technique. However, for carefully chosen bias conditions that reduce this additional resistance to small values, the technique provides reliable results, useful to investigate the graphene-metal contact properties and their technology dependence.
A Note on the LDLT Decomposition of Matrices from Saddle-Point Problems

Sparse linear systems Kx=b are considered, where K is a specially structured symmetric indefinite matrix. These systems arise frequently, e.g., from mixed finite element discretizations of PDE problems. The LDLT factorization of K with diagonal D and unit lower triangular L is known to exist for natural ordering of K, but the resulting triangular factors can be rather dense. On the other hand, for a given permutation matrix P, the LDLT factorization of PTKP may not exist. In this paper a new way to obtain a fill-in minimizing permutation based on initial fill-in minimizing ordering is introduced. For an important subclass of matrices arising from mixed and hybrid finite element discretizations, the existence of the LDLT factorization of the permuted matrix is proved. Experimental results on practical problems indicate that the amount of computational savings can be substantial when compared with the approach based on Schur complement.
Characterization of mast cells residing in cutaneous neurofibromas.

Mast cell Neurofibroma Histamine release Ryoichi Kamide, MD, Department of Dermatology, The Jikei University School of Medicine, Nishishinbashi 3-19-18, Minatoku, Tokyo 105 (Japan) showed a comparable histamine release to those from normal skin in response to nonimmunologic stimuli. The maximum net histamine release from neurofibroma-derived mast cells stimulated by A23187 and compound 48/80 was 23.4 ± 11.0 and 12.0 ± 1.8%, respectively, while that of normal skin was 38.5 and 11.5 ± 3.0%, respectively. Comments This study confirms that cutaneous neurofíbromas in patients with neurofibromatosis contain a large number of mast cells. Cutaneous mast cell suspension, which efficiently responds to nonimmunologic secretory stimuli, was obtained by enzymatic dispersion of neurofíbromas. These mast cells may provide a new approach to the elucidation of the etiological roles of mast cells in the development of neurofíbromas in neurofibromatosis [4] and an experimental source of human connective tissue mast cells for the investigation of mast cell-mediated cutaneous inflammation. References Benyon RC et al: Human mast cells: Their dispersion, purification, and secretory characterization. J Immunol 1987;138:861–867. Lawrence ID et al: Purification and characterization of human skin mast cells: Evidence for human mast cell heterogeneity. J Immunol 1987:139:3062–3069. Tharp MD et al: Functional heterogeneity of human mast cells from different anatomic sites: In vitro responses to morphine sulfate. J Allergy Clin Immunol 1987;79:646–653. Riccardi VM: Mast-cell stabilization to decrease neurofibroma growth. Arch Dermatol 1987;123:1011–1016. Introduction s rHeterogeneity of mast cells derived from different rspecies and anatomic sites has been demonstrated in ¢recent years [1–3]. Increased numbers of cutaneous mast Acells have been observed not only in mastocytosis but also tin several cutaneous neoplasms, including neurofíbromas, and in various inflammatory conditions. In this study, weexamined the mast cell population density and histaminecontent in cutaneous neurofíbromas. In addition, the invitro
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

Dating Wood Rot Specific lineages within the basidiomycete fungi, white rot species, have evolved the ability to break up a major structural component of woody plants, lignin, relative to their non–lignin-decaying brown rot relatives. Through the deep phylogenetic sampling of fungal genomes, Floudas et al. (p. 1715; see the Perspective by Hittinger) mapped the detailed evolution of wood-degrading enzymes. A key peroxidase and other enzymes involved in lignin decay were present in the common ancestor of the Agaricomycetes. These genes then expanded through gene duplications in parallel, giving rise to white rot lineages. The enzyme family that enables fungi to digest lignin expanded around the end of the coal-forming Carboniferous period. Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
Joint attention revisited: Finding strengths among children with autism

Differences in joint attention are prominent for some children with autism and are often used as an indicator of the disorder. This study examined the joint attention competencies of young children with autism who demonstrated joint attention ability and compared them to children with developmental delays. A total of 40 children with autism and developmental delays were matched pairwise based on mental and chronological age. Videos of children engaging in play were coded for the frequency and forms (eye contact, gestures, affect, etc.) of joint attention. Additionally, concurrent language was compared among children with autism (N = 32) by their joint attention ability. Children with autism spectrum disorder entered into joint attention significantly less often than children with developmental delays, but once engaged used the forms of joint attention similarly. For the matched pairs, there were no differences in language, but the children with autism who used joint attention had significantly better language than children with autism who did not (even after controlling for mental age). There is a group of young children with autism who can use joint attention but do so at lower frequencies than children with developmental delays. Possible reasons include difficulty disengaging attention and limited intrinsic social motivation to share. Adult persistence is recommended to encourage joint attention.
Potentiation of C 1 Esterase Inhibitor by StcE , a Metalloprotease Secreted by Escherichia coli O 157 : H 7

The complement system is an essential component of host defense against pathogens. Previous research in our laboratory identified StcE, a metalloprotease secreted by Escherichia coli O157: H7 that cleaves the serpin C1 esterase inhibitor (C1-INH), a major regulator of the classical complement cascade. Analyses of StcE-treated C1-INH activity revealed that surprisingly, StcE enhanced the ability of C1-INH to inhibit the classical complement-mediated lysis of sheep erythrocytes. StcE directly interacts with both cells and C1-INH, thereby binding C1-INH to the cell surface. This suggests that the augmented activity of StcE-treated C1-INH is due to the increased concentration of C1-INH at the sites of potential lytic complex formation. Indeed, removal of StcE abolishes the ability of C1-INH to bind erythrocyte surfaces, whereas the proteolysis of C1-INH is unnecessary to potentiate its inhibitory activity. Physical analyses showed that StcE interacts with C1-INH within its aminoterminal domain, allowing the unaffected serpin domain to interact with its targets. In addition, StcE-treated C1-INH provides significantly increased serum resistance to E. coli K-12 over native C1-INH. These data suggest that by recruiting C1-INH to cell surfaces, StcE may protect both E. coli O157:H7 and the host cells to which the bacterium adheres from complement-mediated lysis and potentially damaging inflammatory events.
Role of tobacco smoking in the causation of chronic respiratory disease.

IN a study of chronic respiratory disease recently undertaken by us in the city of Berlin, New Hampshire,1 the prevalence of various forms of respiratory disease according to age, sex, current tobacco-smoking habits and lifetime cigarette consumption was determined. A questionnaire was administered in conjunction with simple tests of pulmonary ventilation to a probability sample of Berlin residents twenty-five to seventy-four years of age. This paper analyzes the relation between smoking and respiratory disease by examination of the extent of the increased rate of disease in smokers and the relation of disease to increasing use of cigarettes and lifetime exposure .