Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-Validation for Linear Model with Unequal Variances in Genomic Analysis

Abstract In recent years, genomic studies are usually conducted to identify genes that may have an impact on clinical outcomes. The identified genes are then used to establish a predictive model for identifying subjects who are most likely to respond to the test treatment in clinical trials. This information is useful in early and later phases of clinical development. The United States Food and Drug Administration (FDA) requires that such a predictive model be validated before it can be used in clinical development. Shao [Shao, J. (1993). Linear model selection by cross-validation. J. Amer. Statist. Assoc. 88(422):486–494] proposed a cross-validation method for linear model with equal variances, which is found useful in genomic studies. In practice, however, genomic data may be obtained from different sources with unequal variances. As a result, Shao’s method may not be applied directly. In this paper, we extend Shao’s method for cross-validation of a linear model with unequal variances. Along this line, two re-sampling methods were proposed to account for the heterogeneity in variance. Several simulations were performed to evaluate the finite samples performances of the proposed methods. An example concerning a breast cancer research is present to illustrate the use of the proposed methods.
Positive Changes Experienced After a First Episode of Psychosis: A Systematic Review.

OBJECTIVE Although the negative consequences associated with first-episode psychosis (FEP) have been well investigated, relatively less is known about positive changes that people may experience after FEP. Existing literature is disparate and in need of synthesis. Such a synthesis can inform the design of mental health services that foster strengths, hope, and optimism. The objective of this study was to synthesize the literature on how positive change is experienced after FEP by affected persons and their families and friends and to delineate the individual, social, and structural factors facilitating positive change. METHODS A librarian-assisted systematic review of quantitative, qualitative, and mixed-methods studies published in English between 1970 and 2015 was conducted. Articles identified from three databases (PubMed, PsycINFO, and Embase) and through additional search strategies were screened. Results sections were open coded and analyzed by using thematic synthesis. RESULTS Of the 2,777 studies identified, 40 were retained. The synthesis of findings showed that after FEP, service users and their families and friends experienced positive changes at the individual (for example, more insight and clarity), interpersonal (for example, improved relationships), and spiritual levels (for example, greater religiosity). In addition to being facilitated by mental health services, these positive changes were enabled by personal (for example, motivation), social (for example, family support), and spiritual (for example, prayer) factors. CONCLUSIONS Suffering is a core experience of FEP from which a range of positive changes can follow among service users and their families and friends. It may be beneficial for mental health services to specifically strive to promote these positive changes.
Chronic hepatitis C virus infection established and maintained in chimpanzees independent of dendritic cell impairment

Chronic hepatitis C virus (HCV) infection in humans is associated with an impairment of dendritic cells (DC). It has been hypothesized that impairment of DC function may be a central mechanism facilitating the establishment of a chronic carrier state. However, the majority of patients studied with DC impairment to date have been identified and, thus, inadvertently selected because of clinical manifestations leading to their diagnosis, which may have been many years following actual infection. We set out to determine whether impaired DC function occurred in the earlier asymptomatic phase of infection and turned to a well‐defined cohort of HCV‐infected chimpanzees in which the specific date of infection and the nature of the inoculum were well characterized. Results revealed that, in contrast to the observations in human subjects with advanced clinical hepatitis, there was neither impairment of the allostimulatory capacity of monocyte‐derived DC from HCV chronic carriers nor impairment of the maturation process. Decreased allostimulatory capacity was only detected in 2 animals and, interestingly, in those that possessed the highest viral loads. Nevertheless, HCV sequences were undetectable in any of the DC derived from HCV‐infected chimpanzees. In conclusion, these findings suggest that the mechanisms of establishing persistent HCV infection are separate and independent from those responsible for impaired DC function. Indeed, the maturation and allostimulatory impairment, as described in patient studies, are not necessary prerequisites but rather possible consequences of persistent and active HCV infection associated with disease progression. (Hepatology 2003;38:851–858).
An ethical code for everybody in health care

Editor—Ethics are not optional in medicine: they are an essential and integral part of health care. A common ethical code for everybody involved in health care, as proposed by Berwick et al,1 is potentially valuable and is to be welcomed, but the role and limitations of such a code need to be recognised. An ethical code cannot provide the answer to specific ethical problems. Rather than dictating particular actions a code should describe the ethical environment for the delivery of health care and reflect its character and general approach. An ethical code should not try to make subjective aspects of care more objective or separate value from practical situations: it is in the nature of the work of professions that there remains individual responsibility for ethical practice. If challenged, ethical codes cannot explain why moral judgments should be made or give a firm justification for making those judgments; considered, individual moral judgments themselves are more basic and require no more profound reference. Ethical codes can give shape and structure to our moral environment and summarise our ethical position while leaving ethical responsibility with the individual practitioner. Looked at in this way, individual variation and personal issues can be taken into account. An ethical code can facilitate the discussion of ethical issues in difficult cases, and distinctive ethical positions can be established and argued, leading to broader and more secure moral conclusions. An ethical code can describe the ethical attitudes that are shared by healthcare workers, and in this it can be immensely valuable and influential. But what it cannot do is provide the certain answers for the many ethical problems encountered in the course of medical practice.
Automatic Generation of Path Covers Based on the Control Flow Analysis of Computer Programs

Branch testing a program involves generating a set of paths that will cover every arc in the program flowgraph, called a path cover, and finding a set of program inputs that will execute every path in the path cover. This paper presents a generalized algorithm that finds a path cover for a given program flowgraph. The analysis is conducted on a reduced flowgraph, called a ddgraph, and uses graph theoretic principles differently than previous approaches. In particular, the relations of dominance and implication which form two trees of the arcs of the ddgraph are exploited. These relations make it possible to identify a subset of ddgraph arcs, called unconstrained arcs, having the property that a set of paths exercising all the unconstrained arcs also cover all the arcs in the ddgraph. In fact, the algorithm has been designed to cover all the unconstrained arcs of a given ddgraph: the paths are derived one at a time, each path covering at least one as yet uncovered unconstrained arc. The greatest merits of the algorithm are its simplicity and its flexibility. It consists in just visiting recursively in combination the dominator and the implied trees, and is flexible in the sense that it can derive a path cover to satisfy different requirements, according to the strategy adopted for the selection of the unconstrained arc to be covered at each recursive iteration. This feature of the algorithm can be employed to address the problem of infeasible paths, by adopting the most suitable selection strategy for the problem at hand. Embedding of the algorithm into a software analysis and testing tool is recommended. >
Further observations on enablement.

We welcome the excellent paper by Mead and colleagues on the characteristics and utility of the concept of enablement.1 Their paper raises two themes, one on the meaning of enablement, and the second on whether its use as a quality measure would be practical and fair. The most interesting issue in the first theme arises from the observation that patients from ethnic minority groups report higher enablement while possibly receiving care that might otherwise be expected to produce the opposite effect (in particular, having shorter consultations). In our papers on the same subject,2,3 we not only found that ethnic minority groups reported higher enablement, but also that the difference was even greater when the consultation took place in the patient's own language.3 This is compatible with Mead et al 's suggestion that ethnic minority patients are more likely to have their possibly different expectations of health care met than are native UK patients,1 but also suggests that these needs are most likely to be met when the cultural context of doctor and patient are well matched. But the situation may well be even more complex. In a small student study in west London, Hindi and Urdu speaking patients appeared to have different understandings of individual items in the patient enablement instrument (PEI), and also showed different levels of respect towards their GPs (S Khan and GK Freeman, unpublished data, 2004). We completely agree with Mead et al that more qualitative work is needed to help …
Paths of entry into alcoholics anonymous: consequences for participation and remission.

BACKGROUND This study compared individuals with alcohol use disorders who, in the first year after initiating help-seeking, entered Alcoholics Anonymous (AA) only, entered professional treatment and AA together, or entered professional treatment only METHODS A sample of initially untreated individuals (N = 362) was surveyed at baseline and 1 year, 3 years, 8 years, and 16 years later. At each contact point, participants described their participation in AA and treatment and their current alcohol-related functioning. They also described their reasons for entering AA and/or treatment and the perceived benefits of these sources of help RESULTS Compared with individuals who initially participated only in treatment but later entered AA, those who entered treatment and AA together participated in AA longer and more frequently and were more likely to achieve remission. Among individuals who initially participated only in AA, those who later entered treatment had poorer remission outcomes than those who did not enter treatment. Longer duration of participation in AA was associated with a higher likelihood of remission at all four follow-ups; individuals who dropped out of AA were more likely to relapse or remain nonremitted. CONCLUSIONS Compared with individuals who participated only in professional treatment in the first year after they initiated help-seeking, individuals who participated in both treatment and AA were more likely to achieve remission. Individuals who entered treatment but delayed participation in AA did not appear to obtain any additional benefit from AA.
Ultrasonography using simple diagnostic criteria vs palpation for the detection of regional lymph node metastases of melanoma.

OBJECTIVES Our aims were (1) to compare the respective ability of ultrasonography and palpation to detect nodal metastasis during initial staging and follow-up in patients having melanomas and (2) to assess, we believe for the first time, which ultrasound criteria should be used to define metastasis in cases of cutaneous or mucosal melanoma. DESIGN Prospective single-center study. Nodal metastasis was confirmed by histopathologic evaluation. SETTING Dermatology and radiology departments of a university hospital. PATIENTS A total of 160 new consecutive patients with stage I to stage III melanoma. INTERVENTION Experienced operators independently performed 391 paired palpation and ultrasonographic examinations. MAIN OUTCOME MEASURES Firm enlarged nodes found on palpation were considered metastatic. On ultrasonographic examination, circular or oval hypoechoic lymph nodes lacking hyperechoic hila were considered metastatic (stringent criteria). Nodes with 2 or fewer of these patterns and other published signs of metastasis (ie, intranodal nodular hypoechoic focus and irregularity of the node margin) were considered suspicious. RESULTS Over the 6-year study period 33 patients developed nodal metastasis. For palpation and ultrasonography using the stringent criteria, respectively, sensitivity was 41.5% (95% confidence interval [95% CI], 29.6-53.5) and 76.9% (95% CI, 66.7%-87.2%) (P<.001) and specificity was 95.7% (95% CI, 93.5%-97.9%) and 98.4% (95% CI, 97.1%-99.8%) (P<.05). Including ultrasonographically suspicious lymph nodes significantly lowered specificity (86.2% [95% CI, 82.5-89.9]) (P<.05) without improving sensitivity. Previous lymphadenectomy had little impact on ultrasonographic findings. CONCLUSION Ultrasonography using stringent criteria of nodal metastasis, which are easy to identify and reliable, is superior to palpation for early detection of regional lymph node metastases of melanoma.
Prevalence and Characterization of Actinobacillus pleuropneumoniae Isolated from Korean Pigs

Actinobacillus pleuropneumoniae causes porcine pleuropneumoniae which is one of severe threats to the swine industry. In total, 54 strains of Actinobacillus pleuropneumoniae were isolated from 443 pigs between 2012 and 2013 in Korea. Isolates were classified into serotypes 1, 2, 5, 7, 12, and unclassified by multiplex PCR. Genotypes of isolates were divided into three groups according to the sequence of the omlA gene. The antimicrobial resistance rate of serotype 1 was slightly higher than that of serotype 5. In conclusion, to block and treat porcine pleuropneumonia, it is necessary to conduct ongoing characterization of A. pleuropneumoniae isolated from pigs.
A numerical pattern synthesis algorithm for arrays

A simple numerical technique for synthesizing array patterns with low sidelobes is described. Unlike classical approaches to this problem, such as the Dolph-Chebyshev method, the technique described is not limited to uniformly spaced linear arrays of isotropic elements. It can be used with an arbitrary collection of elements. The underlying approach is to assume that the given array elements are used as elements of an adaptive array. The main beam is steered in the desired direction by choosing the steering vector for that direction. To reduce sidelobes, a large number of interfering signals is assumed to be incident on the array from the sidelobe region. The power of this method is that it can handle design problems not treatable by any analytical method. This is illustrated for a 33-element linear array of nonuniformly spaced dipoles of varying length, with the axis of each dipole oriented in a different direction. <<ETX>>
Square Patterns in Rayleigh-Benard Convection with Rotation about a Vertical Axis

We present experimental results for Rayleigh-Benard convection with rotation about a vertical axis at dimensionless rotation rates 0{le}{Omega}{le}250 and {epsilon}{equivalent_to}{Delta}T/{Delta}T{sub c}{minus}1{approx_lt}0.2 . Critical Rayleigh numbers and wave numbers agree with predictions of linear-stability analysis. For {Omega}{approx_gt}70 and small {epsilon} the patterns are cellular with local fourfold coordination and differ from the theoretically expected Kueppers-Lortz unstable state. Stable as well as intermittent defect-free square lattices exist over certain parameter ranges. Over other ranges defects dynamically disrupt the lattice but cellular flow and local fourfold coordination is maintained. {copyright} {ital 1998} {ital The American Physical Society}
Correlation of the virulence of Klebsiella pneumoniae K1 and K2 with the presence of a plasmid encoding aerobactin

Nine isolates of Klebsiella pneumoniae belonging to capsular serotypes K1 and K2 were assayed for virulence in mice. Virulent isolates (50% lethal dose of less than 10(3) microorganisms) and avirulent isolates (50% lethal dose of over 10(6) microorganisms) were selected. Supplementation of a defined minimal medium with transferrin markedly reduced the growth of avirulent strains but had no significant effect on the growth of virulent strains. All isolates produced enterochelin, but only production of aerobactin could be correlated with virulence. The genes encoding aerobactin and its receptor protein were located on a 180-kilobase plasmid. They were cloned into the mobilizable vector pSUP202. Homology was demonstrated with the aerobactin operon of the Escherichia coli plasmid pColV-K30. Transfer of the recombinant plasmid pKP4 into an avirulent recipient enhanced virulence by 100-fold. These experiments demonstrated that aerobactin is an essential factor of pathogenicity in K. pneumoniae.
Ontogeny of postcranial robusticity among Holocene hunter-gatherers of southernmost Africa

Ontogenetic patterns in postcranial robusticity were analysed in the skeletons of eighty-two juvenile Later Stone Age hunter-gatherers with estimated ages at death ranging from infancy to late adolescence. Robusticity was quantified from crosssectional geometric properties of diaphyses at sixteen sites throughout the skeleton, using radiography and casting methods. Skeletal growth profiles for strength measures were analysed with locally weighted regression and additional curve fitting to evaluate developmental trajectories. Ethnographic accounts of infancy and childhood in modern Ju/’hoansi (Khoesan) communities provide a culturally relevant interpretive framework for evaluating skeletal correlates of behaviour. This research demonstrates that bone strength properties can be functionally linked to behaviour among juveniles toward the reconstruction of patterns of physical activity among prehistoric children. Postcranial strength measures vary predictably with age such that developmental patterns and timing in appositional growth can be assessed reliably. The onset of walking among Later Stone Age juveniles is evident by two years of age from proportional lower to upper limb strength measures. The lower limb continues to adapt to increasing loading demands, especially in response to torsional forces, and bending in the medio-lateral plane; biomechanical shape measures illustrate the gradual development of the femoral pilaster. Individual humeral strength is symmetrical with respect to the orientation of maximal bending forces experienced throughout development, but the magnitude of functional adaptive response is greater, on average, in the right limb with more than 70% of the sample over the age of six illustrating right-side dominance. Humeral asymmetry and side dominance does not emerge until late childhood, and the majority of arm strength is accrued during adolescence, relative to average values among Later Stone Age adults. Evidence for sexual dimorphism in upper limb properties is evident by late adolescence whereas sex-based patterns of mobility reflected in lower limb strength have yet to emerge. These results illustrate the developmental patterns that underlie postcranial markers of subsistence activities in Later Stone Age hunter-gatherers.
The antitumor effect of a novel angiogenesis inhibitor (an octahydronaphthalene derivative) targeting both VEGF receptor and NF‐κB pathway

Development of a novel type of angiogenesis inhibitor will be essential for further improvement of therapeutics against cancer patients. We examined whether an octahydronaphthalene derivative, AMF‐26, which was screened as an inhibitor of intercellular adhesion molecule‐1 (ICAM‐1) production stimulated by inflammatory stimuli in vascular endothelial cells, could block angiogenesis in response to vascular endothelial growth factor (VEGF) and/or inflammatory cytokines. Low dose AMF‐26 effectively inhibited the tumor necrosis factor‐α (TNF‐α)‐ or the interleukin‐1β (IL‐1β)‐induced production of ICAM‐1 in human umbilical vascular endothelial cells (HUVECs). We found that the TNF‐α‐induced phosphorylation of nuclear factor of kappa light polypeptide gene enhancer in B‐cells inhibitor, alpha (IκBα) and nuclear translocation of p65 were impaired by AMF‐26 in both endothelial cells and cancer cells. AMF‐26 was found to inhibit the phosphorylation of VEGF receptor 1 (VEGFR1), VEGFR2 and the downstream signaling molecules Akt, extracellular signal‐regulated kinase (ERK)1/2 stimulated by VEGF in HUVECs. Therefore, the VEGF‐induced proliferation, migration and tube formation of vascular endothelial cells was highly susceptible to inhibition by AMF‐26. Oral administration of AMF‐26 significantly blocked VEGF‐ or IL‐1β‐induced angiogenesis in the mouse cornea, and also tumor angiogenesis and growth. Together, our results indicate that AMF‐26 inhibits angiogenesis through suppression of both VEGFR1/2 and nuclear factor‐κB (NF‐κB) signaling pathways when stimulated by VEGF or inflammatory cytokines. AMF‐26 could be a promising novel candidate drug for cancer treatments.
SATELLITE FISH FORECASTING IN SOUTH CHINA SEA

Fish forecasting technology has been applied successfully in many countries. However, most of the forecasting methods used in temperate water were unsuitable to be applied in this region. A fish forecasting model suitable to tropical environment has to be developed. This major project involving several objectives and phases to meet the goal of developing a satellite-based fishery forecasting system in the South China Sea is aimed at supporting the national aspirations of developing an efficient offshore fishery. More importantly, it is aimed at providing the basis for alternate ways towards meeting sustainable harvest of fishery resources. The project is now complete, with most of the major objectives met. Project deliverables include an efficient extraction algorithm of sea surface temperature from AVHRR satellite data which includes an automatic geocoding and cloud masking. Model for extracting ocean colour from SeaWifs was also developed. Based from the multi criteria analysis of these oceanographic conditions, a model suitable for the determination of potential fishing zone in tropical water has been developed. This model is then incorporated into a decision support tool referred as the Tropical Fish Forecasting System (TroFFS). TroFFS is a straight forward and easy to learn software tool that will allow user to process and forecast the potential fishing zone. TroFFS builds upon remote sensing and GIS technology by incorporating aspects of PCI's EASI/PACE and ArcView. In an additional capacity, TroFFS can also be used to detect the warm temperature front and the boundaries of upwelling areas. It is best for the prediction of fishing grounds formed by t he oceanographic phenomenon. TroFFS is a cost-effective geomatics system designed specifically for fish forecasting in tropical waters. TroFFS combines remote sensing and spatial analysis functionality with user-guided fish forecasting processes within a f ully customizable and expandable environment. The system can be integrated with the ground satellite receiving that enabling real time fish forecasting and further developed into the National Fish Forecasting System.