Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurately Counting Singular Values of Bidiagonal Matrices and Eigenvalues of Skew-Symmetric Tridiagonal Matrices

We have developed algorithms to count singular values of a real bidiagonal matrix which are greater than a specified value. This requires the transformation of the singular value problem to an equivalent symmetric eigenvalue problem. The counting of singular values is paramount in the design of bisection- and multisection-type algorithms for computing singular values on serial and parallel machines. The algorithms are based on the eigenvalues of BBt, BtB, and the 2n x 2n zero--diagonal tridiagonal matrix which is permutationally equivalent to the Jordan--Wielandt form [{\scriptsize ${0 \atop B^t}{B \atop 0}$}], where B is an n x n bidiagonal matrix. The two product matrices, which do not have to be formed explicitly, lead to the progressive and stationary qd algorithms of Rutishauser. The algorithm based on the zero--diagonal matrix, which we have named the Golub--Kahan form, may be considered as a combination of both the progressive and stationary qd algorithms. We study important properties such as the backward error analysis, the monotonicity of the inertia count and the scaling of data which guarantee the accuracy and integrity of these algorithms. For high relative accuracy of tiny singular values, the algorithm based on the Golub--Kahan form is the best choice. However, if such accuracy is not required or requested, the differential progressive and differential stationary qd algorithms with certain modifications are adequate and more efficient. We also show how to transform the real skew-symmetric tridiagonal eigenvalue problem to a real bidiagonal singular value problem. Thus, the eigenvalues of a skew-symmetric matrix can be readily counted using algorithms developed here for bidiagonal matrices.
An Object-Oriented Approach to the Design of a User Interface for a Sparse Matrix Package

The authors designed and implemented a sparse matrix package called Sparspak in the late 1970s. One of the important features of that package is an interface which shields the user from the complicated calling sequences common to most sparse matrix software. The implementation of the package was challenging because the relatively primitive but widely available Fortran 66 language was used. Modern programming languages such as Fortran-90 and C++ have important features which facilitate the design of flexible and ``user-friendly'' interfaces for software packages. These features include dynamic storage allocation, function name overloading, user-defined data types, and the ability to hide functions and data from the user. This article describes the redesign of the Sparspak user interface using Fortran-90 and C++, outlining the reasons for its various features and highlighting similarities and differences in the features and capabilities of the two languages. The two new implementations of Sparspak have been named Sparspak-90 and Sparspak++.
A sporadic community-acquired legionnaires disease linked to a domestic hot water supply: Report of a documented case

It is estimated that each year 8,000 to 18,000 cases of Legionnaires disease occur in the United States, most of them sporadic [1]. Unlike most pneumonias caused by infectious agents, legionella infections are not transmitted from person to person but from contaminated environmental reservoirs. The epidemiologic links between the source of infection and sporadic communityacquired Legionnaires disease are seldom established [2,3]. Residential, large-volume hot water systems from multi-dwelling residences have been associated with significant legionellae colonization. A survey in Chicago found Legionella pneumophila in 32% of 95 sampled residences [4]. Ninety-two percent of the residences surveyed were apartment buildings, where hot water is typically provided by large-capacity water heaters and is distributed through extensive plumbing systems. We report a community-acquired sporadic L. pneumophila serogroup 1 pneumonia epidemiologically linked to a single-dwelling, home electric hot water supply.
Circular Distance Two Labeling and the lambda-Number for Outerplanar Graphs

Let G be a graph. A circular distance two labeling with span k is a function $f: V(G) \to \{0, 1, 2, \ldots, k-1\}$ such that (1) $2 \leq |f(u)-f(v)| \leq k-2$ if u and v are adjacent and (2) $f(u) \neq f(v)$ if u and v are of distance two apart. We denote by $\lambda_c(G)$ the smallest span of a circular distance two labeling for G. Let $\Delta(G)$ be the maximum degree of G. We prove, for any outerplanar graph G with $\Delta(G) \geq 15$, $\lambda_c(G)=\Delta(G) +3$. It is also shown that there exist outerplanar graphs G with $\Delta(G) = 2, 3, 4, 5$ for which $\lambda_c(G) = \Delta(G) +4$. Moreover, we prove that $\lambda_c(G) \leq \Delta(G) +5$ for any triangulated outerplanar graph, $\lambda_c(G) \leq \Delta(G) +7$ for any outerplanar graph, and $\lambda_c(G) \leq \Delta(G) +4$ for any outerplanar graph with $\Delta(G) \geq 11$. Immediate consequences of our results include that $\lambda(G) \leq \Delta(G) + 2$ for any outerplanar graphs with $\Delta(G) \geq 15$, where $\lambda(G)$ is the minimum k of a k-L(2, 1)-labeling (or distance two labeling) for G.
Independent and opposite associations of trunk and leg fat depots with adipokines, inflammatory markers, and metabolic syndrome in middle-aged and older Chinese men and women.

OBJECTIVE The objective was to investigate associations of regional fat depots with adipokines, inflammatory markers, and risk of metabolic syndrome (MetS) in a Chinese population. DESIGN AND METHODS Trunk and leg fat mass were determined in a population-based sample of 1150 Chinese (479 men and 671 women) aged 50-70 yr by using whole-body dual-energy x-ray absorptiometry scan. Plasma adiponectin, plasminogen activator inhibitor-1 (PAI-1), retinol-binding protein 4 (RBP4), resistin, C-reactive protein, and IL-6 were measured. The updated National Cholesterol Education Program Adult Treatment Panel III criterion for Asian Americans was used to define MetS. RESULTS Larger body-size adjusted trunk fat mass was significantly associated with lower adiponectin and higher PAI-1, RBP4, C-reactive protein, and IL-6 levels in both genders (P < 0.05). Larger body-size adjusted leg fat mass was significantly associated with higher adiponectin levels in both genders but lower RBP4 and PAI-1 concentrations in men (P < 0.05). Comparing with the lowest body-size adjusted leg fat mass tertile, the odds ratio (95% confidence interval) of MetS in the highest tertile was 0.33 (0.18-0.62; P for trend <0.001) for men and 0.43 (0.28-0.65; P for trend <0.001) for women. The association was attenuated with further controlling adipokines and inflammatory markers (P = 0.09 for men and P = 0.004 for women). CONCLUSION In contrast to trunk fat, large leg fat appears to have favorable effects on adipokines, inflammatory markers, and MetS risk among Chinese. The opposite associations between regional fat depots and MetS risk may partially mediated by adipokines and inflammatory status.
High-resolution peripheral quantitative computed tomographic imaging of cortical and trabecular bone microarchitecture in patients with type 2 diabetes mellitus.

CONTEXT Cross-sectional epidemiological studies have found that patients with type 2 diabetes mellitus (T2DM) have a higher incidence of certain fragility fractures despite normal or elevated bone mineral density (BMD). OBJECTIVE In this study, high-resolution peripheral quantitative computed tomography was applied to characterize cortical and trabecular microarchitecture and biomechanics in the peripheral skeleton of female patients with T2DM. DESIGN AND SETTING A cross-sectional study was conducted in patients with T2DM recruited from a diabetic outpatient clinic. PARTICIPANTS Elderly female patients (age, 62.9 ± 7.7 yr) with a history of T2DM (n = 19) and age- and height-matched controls (n = 19) were recruited. OUTCOME MEASURES Subjects were imaged using high-resolution peripheral quantitative computed tomography at the distal radius and tibia. Quantitative measures of volumetric (BMD), cross-sectional geometry, trabecular and cortical microarchitecture were calculated. Additionally, compressive mechanical properties were determined by micro-finite element analysis. RESULTS Compared to the controls, the T2DM cohort had 10% higher trabecular volumetric BMD (P < 0.05) adjacent to the cortex and higher trabecular thickness in the tibia (13.8%; P < 0.05). Cortical porosity differences alone were consistent with impaired bone strength and were significant in the radius (>+50%; P < 0.05), whereas pore volume approached significance in the tibia (+118%; P = 0.1). CONCLUSION The results of this pilot investigation provide a potential explanation for the inability of standard BMD measures to explain the elevated fracture incidence in patients with T2DM. The findings suggest that T2DM may be associated with impaired resistance to bending loads due to inefficient redistribution of bone mass, characterized by loss of intracortical bone offset by an elevation in trabecular bone density.
Fatherhood in tall men treated with high-dose sex steroids during adolescence.

BACKGROUND/OBJECTIVE Sex steroid treatment to reduce final height of tall boys has been available since the 1950s. In women, it has been shown to interfere with fertility. In men, no such data are available. We therefore evaluated fertility and gonadal function in tall men who did or did not receive high-dose androgen treatment in adolescence. METHODS We conducted a retrospective cohort study of 116 tall men, of whom 60 had been treated. Reproductive and gonadal function was assessed by standardized interview, semen analysis, endocrine parameters, ultrasound imaging, and fatherhood. Mean age at treatment commencement was 14.2 yr, and mean follow-up was 21.2 yr. RESULTS Sixty-six men (36 treated and 30 untreated) had attempted to achieve fatherhood. The probability of conceiving their first pregnancy within 1 yr was similar in treated and untreated men (26 vs. 24; Breslow P=0.8). Eleven treated and 13 untreated men presented with a left-sided varicocele (P=0.5). Testicular volume, sperm quality, and serum LH, FSH, and inhibin B levels were comparable between treated and untreated men. However, treated men had significantly reduced serum T levels, adjusted for known confounders [mean (sd) 13.3 (1.8) vs. 15.2 (1.9) nmol/liter; P=0.005). In addition, testicular volume and serum inhibin B and FSH levels in treated men were significantly correlated with age at treatment commencement. CONCLUSION At a mean follow-up of 21 yr after high-dose androgen treatment, we conclude that fatherhood and semen quality in tall treated men are not affected. Serum testosterone levels, however, are reduced in androgen-treated men. Future research is required to determine whether declining testosterone levels may become clinically relevant for these men as they age.
Splanchnic vein thrombosis in myeloproliferative neoplasms

Splanchnic vein thrombosis (SVT) is one of the most important complications of myeloproliferative neoplasms (MPN). Although MPN are common causes of SVT, the pathophysiological mechanisms underlying this predisposition, their epidemiology and natural history are not fully understood. Studies have concentrated on the generalized prothrombotic environment generated by MPN and their relationship with abnormal blood counts, thereby furthering our knowledge of arterial and venous thrombosis in this population. In contrast, there are few studies that have specifically addressed SVT in the context of MPN. Recent research has demonstrated in patients with MPN the existence of factors increasing the risk of SVT such as the presence of the JAK2 V617F mutation and its 46/1 haplotype. Features unique to the circulating blood cells, splanchnic vasculature and surrounding micro‐environment in patients with MPN have been described. There are also abnormalities in local haemodynamics, haemostatic molecules, the spleen, and splanchnic endothelial and endothelial progenitor cells. This review considers these important advances and discusses the contribution of individual anomalies that lead to the development of SVT in both the pre‐neoplastic and overt stage of MPN. Clinical issues relating to epidemiology, recurrence and survival in these patients have also been reviewed and their results discussed.
Cortisol stimulates secretion of dehydroepiandrosterone in human adrenocortical cells through inhibition of 3betaHSD2.

CONTEXT Initiating factors leading to production of adrenal androgens are poorly defined. Cortisol is present in high concentrations within the adrenal gland, and its production rises with growth during childhood. OBJECTIVE Our aim was to characterize the effect of cortisol and other glucocorticoids on androgen secretion from a human adrenocortical cell line and from nonadrenal cells transfected with CYP17A1 or HSD3B2. DESIGN/SETTING This study was performed in cultured cells, at an academic medical center. METHODS The effects of cortisol upon steroid production in human adrenal NCI-H295R cells were measured by immunoassay, tandem mass spectrometry, and thin-layer chromatography. The effects of cortisol upon the activities of 17, 20 lyase and 3βHSD2 were measured in NCI-H295R cells and in transfected COS-7 cells. RESULTS Cortisol markedly and rapidly stimulated dehydroepiandrosterone (DHEA) in a dose-dependent manner at cortisol concentrations ≥50 μM. Cortisone and 11-deoxycortisol were also potent stimulators of DHEA secretion, whereas prednisolone and dexamethasone were not. Treatment with cortisol did not affect expression of CYP17A1 or HSD3B2 mRNAs. Stimulation of DHEA secretion by cortisol was associated with competitive inhibition of 3βHSD2 activity. CONCLUSIONS Cortisol inhibits 3βHSD2 activity in adrenal cells and in COS-7 cells transfected with HSD3B2. Thus, it is possible that intraadrenal cortisol may participate in the regulation of adrenal DHEA secretion through inhibition of 3βHSD2. We hypothesize that a rise in intraadrenal cortisol during childhood growth may lead to inhibition of 3βHSD2 activity and contribute to the initiation of adrenarche.
An Appropriate Subdifferential for Quasiconvex Functions

In this paper we introduce and study a subdifferential that is related to the quasi- convex functions, much as the Fenchel--Moreau subdifferential is related to the convex ones. It is defined for any lower semicontinuous function, through an appropriate combination of an abstract subdifferential and the normal cone to sublevel sets. We show that this "quasiconvex" subdifferential is always a cyclically quasimonotone operator that coincides with the Fenchel--Moreau subdifferential whenever the function is convex, and that under mild assumptions, the density of its domain in the domain of the function is equivalent to the quasiconvexity of the function. We also show that the "quasiconvex" subdifferential of a lower semicontinuous function contains the derivatives of its differentiable quasiaffine supports. As a consequence, it contains the subdifferential introduced by Martinez-Legaz and Sach in a recent paper [J. Convex Anal. , 6 (1999), pp. 1--12]. Several other properties and calculus rules are also established.
Natural history of nonfunctioning pituitary adenomas and incidentalomas: a systematic review and metaanalysis.

CONTEXT The natural history of pituitary incidentalomas (PIs) and nonfunctioning pituitary adenomas (NFPAs) remains poorly understood. OBJECTIVE The objective of the study was to synthesize the literature on the prognostic factors involved in the progression of PIs and NFPAs in patients followed up conservatively. DATA SOURCES We searched MEDLINE, EMBASE, and Cochrane CENTRAL. We sought to identify further studies by reviewing the reference lists from selected studies and reviews and by querying experts. STUDY SELECTION Eligible studies were longitudinal observational cohort studies that enrolled patients with PIs/NFPAs and followed them up without any treatment from the time of detection and reported on mortality, lesion progression, and development of pituitary hormonal deficiency, apoplexy, or visual field defects. DATA EXTRACTION Reviewers working independently and in duplicate determined studies' eligibility and collected descriptive, methodological quality, and outcome data. Event rates per 100 person-years (PYs) and associated 95% confidence intervals (CIs) were estimated from each study and pooled using the random-effects model. DATA SYNTHESIS The 11 included studies had noncomparative single-cohort design. Follow-up duration ranged from 3 to 15 yr. There was a greater tendency for tumor growth in macroadenomas (12.5 per 100 PYs; 95% CI 7.9, 17.2) and in solid lesions (5.7 per 100 PYs; 95% CI 2.3, 9.2) in comparison with microadenomas (3.3 per 100 PYs; 95% CI 2.1, 4.5) and cystic lesions (0.05 per 100 PYs; 95% CI 0.0, 0.2). The development of pituitary apoplexy and worsening of visual field defects were rare. The overall incidence of new endocrine dysfunction was 2.4 per 100 PYs; 95% CI 0.0, 6.4. The majority of these analyses were associated with significant heterogeneity. There was a trend that did not reach statistical significance for greater incidence of pituitary apoplexy and new endocrine dysfunction worsening in macroadenomas compared with microadenomas. The quality of the evidence (risk of bias) was very low due to heterogeneity, methodological limitations, and imprecision caused by the small number of events. CONCLUSIONS Despite the relatively high prevalence of PIs/NFPAs, the evidence on the natural history of these entities is scarce and of low quality. PIs/NFPAs seem to have fairly rare complications that may be more common when lesions are large (>10 mm) and solid.
Cutaneous cryptococcosis in Hodgkin lymphoma

Multiple erythematous dermal nodules developed on the face of a 56-year-old man receiving chemotherapy for stage IV classical Hodgkin lymphoma (HL) (left). He had no fever and the dermal lesions were asymptomatic. Needle aspiration was performed from one of the nodules and the acquired material was submitted for morphological and microbiological analysis. On microscopy of Giemsa-stained smears, round budding yeast cells were seen (right). The yeasts were enveloped by a capsule, which was more easily seen when the cell was contained within a macrophage (panel A, arrows). Narrow-necked buds (panel B, arrows), phagocytosis of fungal spores by foamy macrophages (panel C) and occasional short pseudohyphae (panel D) were noted. The identification of encapsulated yeasts suggested cryptococcus, and fungal cultures of the specimen subsequently yielded Cryptococcus neoformans. To rule out meningoencephalitis, the patient underwent cerebrospinal fluid examination without significant findings. Blood cultures, radiological assessment and serum cryptococcal antigen were negative. After the diagnosis of isolated cutaneous cryptococcosis was established, oral fluconazole 400 mg/day given for nine months resulted in complete resolution of the infection. The association of HL with cryptococcus is linked to impaired cellular immunity caused by HL. Risk factors for cryptococcosis in HL include the presence of cutaneous anergy, lymphocyte count <1 9 10/l, HL duration of more than 12 months, advanced stage disease, corticosteroid therapy and extensive previous treatment. Cutaneous cryptococcosis can occur as infiltrated nodules or plaques, umbilicated papules resembling molluscum contagiosum or pustular or acneiform lesions. Bleeding and ulceration can occur. Skin biopsies reveal granulomas with yeast-packed macrophages or gelatinous changes with mucin and extracellular cryptococci. Although skin lesions typically accompany meningoencephalitis, prodromal lesions may rarely antedate meningoencephalitis by months so that prompt recognition and treatment can avoid life-threatening sequelae.
Interior Gradient and Proximal Methods for Convex and Conic Optimization

Interior gradient (subgradient) and proximal methods for convex constrained minimization have been much studied, in particular for optimization problems over the nonnegative octant. These methods are using non-Euclidean projections and proximal distance functions to exploit the geometry of the constraints. In this paper, we identify a simple mechanism that allows us to derive global convergence results of the produced iterates as well as improved global rates of convergence estimates for a wide class of such methods, and with more general convex constraints. Our results are illustrated with many applications and examples, including some new explicit and simple algorithms for conic optimization problems. In particular, we derive a class of interior gradient algorithms which exhibits an $O(k^{-2})$ global convergence rate estimate.
Surfactant protein-A (SP-A) selectively inhibits prostaglandin F2alpha (PGF2alpha) production in term decidua: implications for the onset of labor.

CONTEXT Labor is characterized by "decidual activation" with production of inflammatory mediators. Recent data suggest that surfactant protein-A (SP-A) may be critical to the onset of labor in mice. Whether this is also true in humans is unclear. OBJECTIVES The aim was to investigate: 1) the expression of SP-A at the maternal-fetal interface; 2) the effect of SP-A on the production of inflammatory mediators by human decidua; and 3) the association between single nucleotide polymorphisms in maternal SP-A genes and spontaneous preterm birth. RESEARCH DESIGN AND METHODS In situ expression of SP-A was investigated by immunohistochemistry and quantitative RT-PCR. Term decidual stromal cells were isolated, purified, and treated with/without SP-A (1-100 μg/ml), IL-1β, and/or thrombin. Levels of inflammatory mediators [IL-6, IL-8, TNFα, matrix metalloproteinase-3, monocyte chemotactic protein-1, IL-1β, PGE(2), prostaglandin F(2α) (PGF(2α))] and angiogenic factors (soluble fms-like tyrosine kinase-1, vascular endothelial growth factor) were measured in conditioned supernatant by ELISA and corrected for protein content. The effect of SP-A on eicosanoid gene expression was measured by quantitative RT-PCR. RESULTS SP-A localized to endometrium/decidua. High-dose SP-A (100 μg/ml) inhibited PGF(2α) by term decidual stromal cells without affecting the production of other inflammatory mediators, and this effect occurred at a posttranscriptional level. Decidual SP-A expression decreased significantly with labor. Single nucleotide polymorphisms in the SP-A genes do not appear to be associated with preterm birth. CONCLUSIONS SP-A is produced by human endometrium/decidua, where it significantly and selectively inhibits PGF(2α) production. Its expression decreases with labor. These novel observations suggest that decidual SP-A likely plays a critical role in regulating prostaglandin production within the uterus, culminating at term in decidual activation and the onset of labor.
A Trust-Region Approach to Nonlinear Systems of Equalities and Inequalities

In this paper, two new trust-region algorithms for the numerical solution of systems of nonlinear equalities and inequalities are introduced. The formulation is free of arbitrary parameters and possesses sufficient smoothness to exploit the robustness of the trust-region approach. The proposed algorithms are one-sided least-squares trust-region algorithms. The first algorithm is a single-model algorithm, and the second one is a multimodel algorithm where the Cauchy point computation is a model selection procedure. Global convergence analysis for the two algorithms is presented. Our analysis generalizes to nonlinear systems of equalities and inequalities the well-developed theory for nonlinear least-squares problems. Numerical experiments on the two algorithms are also presented. The performance of the two algorithms is reported. The numerical results validate the effectiveness of our approach.