Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of PAX‐2, RCC antigen, and antiphosphorylated H2AX antibody (γ‐H2AX) in diagnosing metastatic renal cell carcinoma by fine‐needle aspiration

Diagnosing metastatic renal cell carcinoma (RCC) by fine‐needle aspiration (FNA) can be challenging. Existing antibodies supporting a diagnosis of RCC, including CD10 and RCC‐Ma, have problems with specificity and interpretation. In this report, we evaluate the use of two newer immunostains, PAX‐2 and γ‐H2AX, which to our knowledge have not been studied in FNA material, in the diagnosis of metastatic RCC and in comparison with RCC‐Ma. 29 cases of metastatic RCC were identified as well as a TMA of an additional 30 RCC cases. In the case cohort, RCC‐Ma in a membranous pattern of staining identified 15/27 (56%) metastatic RCC, although interpretation was made difficult in many cases due to focality of staining and non‐specific cytoplasmic staining. PAX‐2 stained 23/29 (79%) of tumors in a nuclear stain, most strongly. Gamma‐H2AX stained 19/26 (73%) of metastatic RCC strongly in a nuclear stain. In the TMA, strong, diffuse nuclear staining with γ‐H2AX was present in 22/30 RCC (73%). If weak staining was also included as positive, 26/30 (87%) were positive. PAX‐2 stained RCC TMA with a lower percentage at 56%, including weaker staining intensity. Both PAX‐2 and γ‐H2AX demonstrated patchy staining of normal renal tubules, PAX‐2 to a greater extent. Both PAX‐2 and γ‐H2AX are sensitive markers for the diagnosis of metastatic RCC, with improved ease of interpretation when compared with RCC‐Ma. A combination of all 3 markers identified 87% of cases, and failure to stain for both PAX‐2 and γ‐H2AX suggests against, but does not disprove, a diagnosis of RCC. Diagn. Cytopathol. 2008; 36: 568–573. © 2008 Wiley‐Liss, Inc.
Identifying Finite Mixtures of Nonparametric Product Distributions and Causal Inference of Confounders

We propose a kernel method to identify finite mixtures of nonparametric product distributions. It is based on a Hilbert space embedding of the joint distribution. The rank of the constructed tensor is equal to the number of mixture components. We present an algorithm to recover the components by partitioning the data points into clusters such that the variables are jointly conditionally independent given the cluster. This method can be used to identify finite confounders.
A Social Network Approach to Examine the Role of Influential Stocks in Shaping Interdependence Structure in Global Stock Markets

This paper investigates the role of influential stocks in shaping the emergent system-level interdependence in global stock markets using a large set of stocks selected from major stock market indices from across the globe. We have proposed a method to identify influential stocks using various centrality measures used in social network analysis literature. Our study shows how these influential stocks provide key linkages in integrating the global stock markets as an interconnected system. We have also shown that the regional influence dominates over the economic sector influence in shaping the topological structure of stock market network. The study also captures the change in the topology of this network following the collapse of Lehman Brothers.
Quality of assessment of prior learning (APL) in university programmes: perceptions of candidates, tutors and assessors

Formal diplomas and certificates have been accepted as proof that students may receive exemption for parts of their educational programme. Nowadays, though, it is socially desirable that informal and non-formal learning experiences are also recognised. Assessment of prior learning (APL) addresses this issue. In APL, the candidate's knowledge, skills or competences required in informal and non-formal learning are measured against a standard to determine whether they match the learning objectives. Although APL is frequently used in workplaces and vocational education, it is practised less in universities, and research is lacking in this context. This study aims to evaluate the first APL procedure in an academic computer science programme, and an adjusted APL procedure in an educational science masters programme. This is done from the perspective of the APL candidates, tutors and assessors, using the theoretical framework by Baartman et al. (2006). The computer science participants comprised 23 candidates from a police software company, four tutors and four assessors. From educational science, nine candidates, two tutors and two assessors participated. The results show that the APL procedure in educational science is viewed significantly more positively than that in computer science; further, the computer science assessors differ considerably from the other participants in their perceptions relating to the quality criterion ‘cognitive complexity’. Explanations for the difference between the two programmes are discussed in this article and assessor and tutor training highly recommended.
Work-family conflict and employee job satisfaction: A comparison of state-owned and foreign-invested enterprises in Vietnam

Work and family issues have been long discussed in academic and practices. Work affects family and personal life and vice versa. The relationship of work and family could lead to positive consequences (e.g. Improved skills, morale) or negative consequences (e.g. Conflict, strain, exhaustion) to employees. The ? aims of this paper is to investigate the effects of work-family conflict on job satisfaction and compare the differences between employees working in State-owned enterprises (SOEs) and Foreign-invested enterprises (FIEs) in Vietnam. Respondents for this study were obtained from 49 employees from SOEs and 35 employees from FIEs in Vietnam. Descriptive analysis, independent-sample t-test and hierarchical regression analysis were conducted to analyse the data. The results of the study reveal that job satisfaction were found to be significantly different, but work-to-family conflict and family-to-work conflict were not significantly differ between the employees from SOEs and FIEs. Moreover, work-to-family conflict (WIF) and family-to-work (FIW) conflict are not the significant predictors for employee job satisfaction in both enterprises. The findings suggest that cultural value affects the link between work-family conflict and job satisfaction to some extent. Research limitation and recommendation for future research on this topic were discussed.
Commentary on End-of-Life Decision-Making in Singapore: Best Interest Conflicting with Surrogate Decision-Making

In patients who have impaired decision-making capacity, an appointed surrogate (extended autonomy) or the best interests standard are used to make medical decisions. When these standards are in conflict with each other, clinicians are left in a conundrum. The case of a patient in a persistent vegetative state is used to illustrate the relevant principles and the conflicts that can arise. It is reviewed through the commentary of a student of medicine, and the role of managing physicians in consensus-building is explored as a potential solution to this dilemma.
Prenatal Hypoxia Leads to Increased Muscle Sympathetic Nerve Activity, Sympathetic Hyperinnervation, Premature Blunting of Neuropeptide Y Signaling, and Hypertension in Adult Life

Adverse conditions prenatally increase the risk of cardiovascular disease, including hypertension. Chronic hypoxia in utero (CHU) causes endothelial dysfunction, but whether sympathetic vasoconstrictor nerve functioning is altered is unknown. We, therefore, compared in male CHU and control (N) rats muscle sympathetic nerve activity, vascular sympathetic innervation density, and mechanisms of sympathetic vasoconstriction. In young (Y)-CHU and Y-N rats (≈3 months), baseline arterial blood pressure was similar. However, tonic muscle sympathetic nerve activity recorded focally from arterial vessels of spinotrapezius muscle had higher mean frequency in Y-CHU than in Y-N rats (0.56±0.075 versus 0.33±0.036 Hz), and the proportions of single units with high instantaneous frequencies (1–5 and 6–10 Hz) being greater in Y-CHU rats. Sympathetic innervation density of tibial arteries was ≈50% greater in Y-CHU than in Y-N rats. Increases in femoral vascular resistance evoked by sympathetic stimulation at low frequency (2 Hz for 2 minutes) and bursts at 20 Hz were substantially smaller in Y-CHU than in Y-N rats. In Y-N only, the neuropeptide Y Y1-receptor antagonist BIBP3226 attenuated these responses. By contrast, baseline arterial blood pressure was higher in middle-aged (M)-CHU than in M-N rats (≈9 months; 139±3 versus 126±3 mm Hg, respectively). BIBP3226 had no effect on femoral vascular resistance increases evoked by 2 Hz or 20 Hz bursts in M-N or M-CHU rats. These results indicate that fetal programming induced by prenatal hypoxia causes an increase in centrally generated muscle sympathetic nerve activity in youth and hypertension by middle age. This is associated with blunting of sympathetically evoked vasoconstriction and its neuropeptide Y component that may reflect premature vascular aging and contribute to increased risk of cardiovascular disease.
TGA transcription factors and jasmonate-independent COI1 signalling regulate specific plant responses to reactive oxylipins

Jasmonates and phytoprostanes are oxylipins that regulate stress responses and diverse physiological and developmental processes. 12-Oxo-phytodienoic acid (OPDA) and phytoprostanes are structurally related electrophilic cyclopentenones, which activate similar gene expression profiles that are for the most part different from the action of the cyclopentanone jasmonic acid (JA) and its biologically active amino acid conjugates. Whereas JA–isoleucine signals through binding to COI1, the bZIP transcription factors TGA2, TGA5, and TGA6 are involved in regulation of gene expression in response to phytoprostanes. Here root growth inhibition and target gene expression were compared after treatment with JA, OPDA, or phytoprostanes in mutants of the COI1/MYC2 pathway and in different TGA factor mutants. Inhibition of root growth by phytoprostanes was dependent on COI1 but independent of jasmonate biosynthesis. In contrast, phytoprostane-responsive gene expression was strongly dependent on TGA2, TGA5, and TGA6, but not dependent on COI1, MYC2, TGA1, and TGA4. Different mutant and overexpressing lines were used to determine individual contributions of TGA factors to cyclopentenone-responsive gene expression. Whereas OPDA-induced expression of the cytochrome P450 gene CYP81D11 was primarily regulated by TGA2 and TGA5, the glutathione S-transferase gene GST25 and the OPDA reductase gene OPR1 were regulated by TGA5 and TGA6, but less so by TGA2. These results support the model that phytoprostanes and OPDA regulate differently (i) growth responses, which are COI1 dependent but jasmonate independent; and (ii) lipid stress responses, which are strongly dependent on TGA2, TGA5, and TGA6. Identification of molecular components in cyclopentenone signalling provides an insight into novel oxylipin signal transduction pathways.
Sense of place in outdoor-pursuits trip groups

Studies have revealed that sense of community and group cohesion increase significantly over time in outdoor-pursuits trip groups. This study sought to understand similar development of sense of place. Do people simultaneously become more attached to or dependent on the natural environment as they grow closer to each other? Results from a study of college students participating in a 13-day Outdoor Education Practicum course in the Adirondacks (New York) indicate that sense of place is not significantly correlated to sense of community or group cohesion. Sense of place scores remained relatively high across a 2-week course, but did not significantly increase over time. However, beginners had significantly lower scores than intermediates and those with advanced skills on Day 11; no differences were detected among levels of development (e.g., skill, experience, commitment) by Day 13. Perhaps the course was not long enough to cause a significant change. Alternatively, placing as much emphasis on developing an attachment to the natural world as on building a sense of community might influence similar growth in sense of place.
Herschel : the first science highlights Special feature L etter to the E ditor Herschel ATLAS : The cosmic star formation history of quasar host galaxies

We present a derivation of the star formation rate per comoving volume of quasar host galaxies, derived from stacking analyses of far-infrared to mm-wave photometry of quasars with redshifts 0 < z < 6 and absolute I-band magnitudes −22 > IAB > −32 We use the science demonstration observations of the first ∼ 16 deg2 from the Herschel Astrophysical Terahertz Large Area Survey (H-ATLAS) in which there are 240 quasars from the Sloan Digital Sky Survey (SDSS) and a further 171 from the 2dF-SDSS LRG and QSO (2SLAQ) survey. We supplement this data with a compilation of data from IRAS, ISO, Spitzer, SCUBA and MAMBO. H-ATLAS alone statistically detects the quasars in its survey area at > 5σ at 250, 350 and 500 μm. From the compilation as a whole we find striking evidence of downsizing in quasar host galaxy formation: low-luminosity quasars with absolute magnitudes in the range −22 > IAB > −24 have a comoving star formation rate (derived from 100 μm rest-frame luminosities) peaking between redshifts of 1 and 2, while high-luminosity quasars with IAB < −26 have a maximum contribution to the star formation density at z ∼ 3. The volume-averaged star formation rate of −22 > IAB > −24 quasars evolves as (1 + z)2.3±0.7 at z < 2, but the evolution at higher luminosities is much faster reaching (1 + z)10±1 at −26 > IAB > −28. We tentatively interpret this as a combination of a declining major merger rate with time and gas consumption reducing fuel for both black hole accretion and star formation.
An Integrative Method for Accurate Comparative Genome Mapping

We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying “maximal similar segments,” and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating reorder-free segments and identifying orthologous segments. In the process, MAGIC efficiently handles ambiguities resulting from duplications that occurred before the speciation of the considered organisms from their most recent common ancestor. We demonstrate both MAGIC's robustness and scalability: the former is asserted with respect to its initial input and with respect to its parameters' values. The latter is asserted by applying MAGIC to distantly related organisms and to large genomes. We compare MAGIC to other comparative mapping methods and provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations, such as indels and duplications, including explicitly transposable and phagic elements. The strength of our method is demonstrated by detailed statistics computed for each type of these large-scale mutations. MAGIC enabled us to conduct a comprehensive analysis of the different forces shaping prokaryotic genomes from different clades, and to quantify the importance of novel gene content introduced by horizontal gene transfer relative to gene duplication in bacterial genome evolution. We use these results to investigate the breakpoint distribution in several prokaryotic genomes.
Assessment of osteoporosis by quantitative ultrasound versus dual energy X-ray absorptiometry in children with chronic rheumatic diseases.

OBJECTIVE To evaluate the validity of quantitative ultrasound bone sonometry (QUBS) as a screening tool for the diagnosis of osteoporosis in children with chronic rheumatic diseases (CRD), compared to the conventional dual energy x-ray absorptiometry (DEXA). METHODS Forty children with CRD [32 with juvenile idiopathic arthritis (JIA), 6 with systemic lupus erythematosus, and 2 with dermatomyositis] aged 9.9 +/- 4.3 years, were evaluated by QUBS of radius and tibia and DEXA of the lumbar spine. Twenty-five (62.5%) patients were treated with corticosteroids. Measurements of the velocity of the ultrasound wave, expressed as speed of sound (SOS) in m/s, and the results of the bone mineral density (BMD) assessed by DEXA were compared to reference data from healthy age and sex matched Israeli children. RESULTS Compared to controls, patients with CRD had significantly lower values by QUBS and DEXA alike. BMD and SOS z scores < -1 SD were found in 45% and 38% of the patients, respectively. Reduced BMD and SOS values correlated with age at disease onset and corticosteroid treatment. BMD alone correlated negatively with disease duration and methotrexate therapy. BMD was significantly lower in patients with polyarticular JIA compared to patients with oligoarticular disease (p < 0.03). SOS values did not differ between subtypes of JIA. A significant positive correlation was found between the lumbar DEXA and radius SOS. CONCLUSION QUBS evaluation of radius and tibia yielded results comparable to DEXA and may therefore be used for screening patients with CRD for osteoporosis. QUBS might represent a promising means of evaluating bone quality in at-risk children.
The Modulation of Mitochondrial Nitric-oxide Synthase Activity in Rat Brain Development*

Different mitochondrial nitric-oxide synthase (mtNOS) isoforms have been described in rat and mouse tissues, such as liver, thymus, skeletal muscle, and more recently, heart and brain. The modulation of these variants by thyroid status, hypoxia, or gene deficiency opens a broad spectrum of mtNOS-dependent tissue-specific functions. In this study, a new NOS variant is described in rat brain with an M r of 144 kDa and mainly localized in the inner mitochondrial membrane. During rat brain maturation, the expression and activity of mtNOS were maximal at the late embryonic stages and early postnatal days followed by a decreased expression in the adult stage (100 ± 9versus 19 ± 2 pmol of [3H]citrulline/min/mg of protein, respectively). This temporal pattern was opposite to that of the cytosolic 157-kDa nNOS protein. Mitochondrial redox changes followed the variations in mtNOS activity: mtNOS-dependent production of hydrogen peroxide was maximal in newborns and decreased markedly in the adult stage, thus reflecting the production and utilization of mitochondrial matrix nitric oxide. Moreover, the activity of brain Mn-superoxide dismutase followed a developmental pattern similar to that of mtNOS. Cerebellar granular cells isolated from newborn rats and with high mtNOS activity exhibited maximal proliferation rates, which were decreased by modifying the levels of either hydrogen peroxide or nitric oxide. Altogether, these findings support the notion that a coordinated modulation of mtNOS and Mn-superoxide dismutase contributes to establish the rat brain redox status and participate in the normal physiology of brain development.
PD-L1 expression on malignant cells is no prerequisite for checkpoint therapy

ABSTRACT Immunotherapy with PD-1/PD-L1-blocking antibodies is clinically effective for several tumor types, but the mechanism is not fully understood. PD-L1 expression on tumor biopsies is generally regarded as an inclusion criterion for this cancer therapy. Here, we describe the PD-L1-blocking therapeutic responses of preclinical tumors in which PD-L1 expression was removed from cancer cells, but not from immune infiltrate. Lack of PD-L1 expression on malignant cells delayed tumor outgrowth in a CD8+ T cell-mediated fashion, showing the importance of this molecule in immune suppression. PD-L1 expression was evident on myeloid-infiltrating cells in the microenvironment of these tumors and targeting stromal PD-L1 with blocking antibody therapy had additional antitumor effect, demonstrating that PD-L1 on both malignant cells and immune cells is involved in the mechanism of immunotherapeutic antibodies. Importantly, comparable results were obtained with PD-1-blocking therapy. These findings have implications for inclusion of cancer patients in PD-1/PD-L1 blockade immunotherapies.
Testability of Object-Oriented Systems: a Metrics-based Approach

'U' means rabbits, 'zu' means figure, 'maki' means rotation, and 'Uzumaki' means spirals or swirls. Yellow represents the color of the moon in Japan and it is imagined (though not seriously) that rabbits live in the moon and make mochi (food made from rice). Akiyoshi Kitaoka describing the meaning of 'Uzumaki' on his web site. The drawing appeared in his Japanese book Trick Eyes 2, and quickly became popular on the Internet. Preface When I first saw the 'Uzumaki' drawing, it struck me how well it captured my state of mind at the beginning of the work on this thesis. The topic I had chosen to explore appeared to be huge and very difficult, and many things of interest were scattered throughout it. I was unsure where to focus my attention. One cannot help but feel the same way when looking at 'Uzu-maki'; wherever one looks, there is always something going on in another part of the drawing. Hence I decided to put 'Uzumaki' on the cover of my thesis. However, the analogy does not stop there. If one can resist the urge to keep looking at the moving wheels of 'Uzumaki', and focus on only one, all the wheels will eventually stop moving. This thesis is the result of focusing on one particular aspect of the topic, testability. I thank my coaches, Tobias Kuipers and Arie van Deursen, for supporting me in resisting the urge to keep looking at the moving wheels. The topic of this thesis was conceived by Arie, who is never short of interesting ideas or new perspectives. Together with Tobias and Paul Klint, it was decided that the project would be performed at the Software Improvement Group. I was amazed how readily Tobias agreed to be my coach, and allowed me to work at the SIG. Arie, Paul and Tobias, thanks a lot for your feedback and support. Working at the SIG has been an excellent experience, for which I'd like to thank my colleagues. In particular, I am grateful to Alex van den Bergh, Helden for allowing me a glimpse of the real world of software engineering. A great advantage of working at a company is the possibility to explore the industry. In my case, I visited a number of people of other companies and interviewed them about their testing efforts. I'd like to thank Joris Alkema, Rutger Buckmann and Vincent van Moppes all …
Electron microscopic studies of brain tumors

THE APPLICATION of electron microscopy to neoplasms of the nervous system has revealed a number of diagnostic characteristics that are of importance in the identification of tumors. Although a thorough description of the ultrastructural details evident in these tumors is beyond the scope of the current account, it would seem useful to call attention to the diagnostic utility of electron microscopy. This utility stems from the fact that all cellular elements are visible in electron micrographs, whereas, by light microscopy, specialized technics are necessary for the demonstration of separate elements. Moreover, by electron microscopy, cellular organelles can be studied with as much precision as was formerly available for cells and tissues, so that pathologic changes in subcellular elements can now be investigated.