Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Decoy Sets for Evaluating Energy Functions

Abstract Energy functions are crucial ingredients of protein tertiary structure prediction methods. Assessing the quality of energy functions is therefore of prime importance. It requires the elaboration of a standard evaluation scheme, whose key elements are: i) sets that contain the native and several non-native structures of proteins (decoys) in order to test whether the energy functions display the expected quality features and ii) measures to evaluate the reliability of energy functions. We present here a survey of the recent advances in these two related fields. In a first part, we analyze and review the large number of decoy sets that are available on the web, and we summarize the characteristics of a challenging decoy set. We then discuss how to define the quality of energy functions and review the measures related to it.
Working in America: A Blueprint for the New Labour Market

theoretical and applied institutionalist ideas. But the book was also intended for the author's professional colleagues and the general public. Because Tool writes with commendable clarity and precision, TDE is well suited for all audiences. Ultimately TDE has stood the test of time because we do live in a discretionary economy. How we collectively evaluate and attempt to change the institutional structure of the discretionary economy is important, and Tool's analysis is far more relevant to the task than the analytical methods offered in the usual textbooks by our neoclassical colleagues. Stated differently, the process of making value judgments about institutions and then changing them is a far more important undertaking than finding the equilibrium price of peanut butter. It is no accident that the phrase "discretionary economy" has become part of the standard vocabulary of institutionalists.
Performance Improvement of Two-Vectors-Based Model Predictive Control of PWM Rectifier

Finite-control-set model predictive control (FCSMPC) has been proposed as a powerful control strategy for the power control of the pulse-width modulation rectifier. However, conventional FCSMPC applies only one voltage vector during one control period, which still presents relatively high power ripples. Introducing a zero vector in combination with a nonzero vector during one control period can improve the steady-state performance of the conventional FCSMPC, but the fixed vector combination is not an optimal solution in minimizing power errors. This paper proposes an improved two-vectors-based MPC, which relaxes the vector combination to two arbitrary voltage vectors. Compared to prior improved MPC with fixed vector combinations, the proposed method achieves better steady-state performance without affecting the dynamic response. Furthermore, the average switching frequency is reduced by up to 29.5% in average. The principles of vector selection and optimal vector duration are introduced in detail. The results obtained from two kinds of three-vectors-based predictive control methods are also presented for the aim of comparison. Both simulation and experimental results confirm the theoretical study and the effectiveness of the proposed method.
Association between pollen hypersensitivity and edible vegetable allergy: a review.

Over the last three decades several authors have described the existence of an association between sensitivity to different pollens and sensitivity to diverse edible vegetables. An association between ragweed pollinosis and hypersensitivity to Cucurbitaceae vegetables (e.g., watermelon, melon, cucumber) and banana has been reported. Other authors have found a relationship between birch pollinosis and sensitization to hazelnut, apple, carrot, potato, kiwi and other vegetables. Additionally, several papers have shown the association between mugwort pollinosis and sensitization to celery, carrot, spices, nuts, mustard and Leguminoseae vegetables. Later, some studies showed association between grass pollinosis and sensitization to tomato, potato, green- pea, peanut, watermelon, melon, apple, orange and kiwi. Finally, an association between sensitization to plantain pollen and melon hypersensitivity was also described. The association between pollinosis and edible vegetable sensitization has been explained by the combination of different hypotheses, such as the following: 1) presence of lectins in edible vegetables; 2) existence of IgE to carbohydrates of the glycoproteins (cross-reactive carbohydrate determinants); and, 3) existence of common allergens between pollens and edible vegetables. Up to now three allergens have been identified as responsible for cross-reactivity in these associations: profilin, a 14 kd protein that regulates actin; Bet v 1, the 18 kd birch pollen allergen; and a 60-69 kd allergen. It is important to study in depth these associated sensitizations and the common allergens responsible for them in order to improve diagnostic methods and treatment of these syndromes.
Mental health in Dutch children: (III) behavioral‐emotional problems reported by teachers of children aged 4–12

Standardized teacher reports on children's behavioral-emotional problems can provide information on areas of children's functioning not readily accessible to other informants such as parents or clinicians. Once we accept the generally low agreement between different informants as inevitable, we may make use of the different types of information available from different sources. To do so we need base-line data from different informants that take account of key demographic variables such as gender, age and socio-economic status. In a previous report we provided such data for parent reported behavioral-emotional problems in children aged 4 through 16. In the present study we reported on the prevalence of a wide range of specific behavioral-emotional problems reported by teachers in a representative sample of 1,162 Dutch children aged 4 through 12; identified differences related to demographic variables and compared our data with those from other population based surveys. We used the Achenbach Teacher's Report Form (TRF) to collect our data because a comparison between different standardized teacher assessment instruments showed the TRF to be the most promising due to its solid psychometric background and its ready applicability. Our data supported the TRF's reliability and validity. For each of the 118 behavioral-emotional problems, the prevalence rates were presented graphically for both genders in two-year age groups. ANCOVAs were performed to assess the main effects and interaction of age and gender with SES as covariate for each problem item and total problem score. Of the demographic variables gender showed most numerous effects on problem items and showed the largest effect on total problem score. The main findings were: Boys obtained higher scores than girls. Many items on which boys scored higher are related to socially disapproved behavior. Boys obtained higher scores on concentration, attention and hyperactivity problems. Boys (especially the younger ones) scored higher on problems related to academic functioning. Teacher reports revealed larger gender differences than parent reports. Both parents and teachers scored boys higher on items predominantly associated with the externalizing syndrome. More boys than girls were attending education in special schools. Age showed no significant effect on total problem score, although older children were scored higher on a number of items associated with academic, somatic and social functioning and with emotions related to inner feelings. (ABSTRACT TRUNCATED AT 400 WORDS)
Rational basis for Trk inhibition therapy for prostate cancer

Prostatic cancer cells are lethal because they acquire the ability to activate survival pathways that do not require androgenic stimulation. As a rational approach to developing effective therapy for these devastating cells, specific signal transduction pathways uniquely required for the survival of these nonandrogen‐dependent prostate cancer cells must be identified. Previous studies suggested that the neurotrophin/trk signal transduction axis may regulate such unique survival pathways. In the present study, the changes in expression of the neurotrophins (NGF, BDNF, and NT‐3) and their cognate receptors (i.e., trk and p75NTR) during the progression of normal prostatic epithelial cells to malignancy were documented. Additionally, the consequences of inhibiting these trk signaling pathways on the in vitro survival of prostate cancer cells was tested.
Suitable for whom? The case of system of rice intensification in Tanzania

ABSTRACT Purpose: This study examines the suitability of the system of rice intensification (SRI) for diverse small-scale farmers in Tanzania by exploring if poor and non-poor farmers adopt the system to a similar extent. Originality: The suitability of low-external input technologies such as SRI for diverse African farmers is a contentious issue. Existing studies suggest that adoption may be skewed away from poorer farmers, but no studies have explicitly categorized farmers who participate in adoption of SRI. Methods: Farmers exposed to SRI were randomly surveyed. Sample farmers were categorized into three socioeconomic groups – wealthier, middle-wealth, and poorer – using factor and cluster analysis approaches. Wealth category is then used in a logit model to determine probabilities of adopting SRI practices across the different groups. Findings: The results indicate that middle-wealth group adopt SRI to a greater extent compared to the wealthier and poorer groups. The extent of adoption by wealthier and poorer groups is similar, although constraining circumstances differ. Access to factors that consistently explained adoption: contact with extension services, land with water, and labor, vary systematically among groups. Theoretical implication: Low adoption is often assumed on reduced exposure to a technology, and non-adopters are expected to eventually adopt. The results suggest, however, that farmers, who have not adopted, may not do so, even after being exposed. SRI as a package does not fit their socioeconomic conditions. Practical implications: To support adoption across all wealth categories, extension should focus on promoting individual practices rather than the package to enable farmers adopt practices that fit their socioeconomic characteristics.
Sexual dimorphism in the aging kidney: Effects on injury and nitric oxide system.

BACKGROUND Male gender confers enhanced susceptibility to development of age-dependent kidney damage. In other models of progressive renal disease, development of injury is linked to declines in renal nitric oxide synthase (NOS) capacity. METHODS We investigated the in vitro characteristics of the renal NOS system in young (3 to 5 months), middle-aged (11 to 13 months) and old (18 to 22 months) male and female Sprague-Dawley rats. RESULTS NOS activity (pmol [3H]-arginine converted to [3H]-citrulline/mg protein/minute) is reduced in the soluble fraction of renal cortex from old versus young males but not females. In contrast, NOS activity in the soluble fraction of cerebellum is not altered by age or gender. The abundance of endothelial NOS (eNOS) and neuronal (nNOS) is reduced in renal cortex of old versus young males but is unchanged in female cortex. In renal medulla, eNOS protein is reduced with age in both males and females. We found no difference in abundance of either eNOS or nNOS protein in the cortex of young male and female rats. The incidence and severity of glomerular damage increases markedly with age in the male and only slightly in the female. CONCLUSION These findings indicate that a relative reduction occurs in renal NOS in the male kidney with advancing age, whereas NOS protein and activity is maintained during aging in females. This, together with the marked age-dependent kidney damage seen in the male, suggests that the renal NO deficiency in the aging male rat may contribute to the age-dependent kidney damage.
Implications of complex adaptive systems theory for the design of research on health care organizations

Background: Because health care organizations (HCOs) are complex adaptive systems (CASs), phenomena of interest often are dynamic and unfold in unpredictable ways, and unfolding events are often unique. Researchers of HCOs may recognize that the subject of their research is dynamic; however, their research designs may not take this into account. Researchers may also know that unfolding events are often unique, but their design may not have the capacity to obtain information from meager evidence. Purpose: These two concerns led us to examine two ideas from organizational theory: (a) the ideas of K. E. Weick (1993) on organizational design as a verb and (b) the ideas of J. G. March, L. S. Sproull, and M. Tamuz (1991) on learning from samples of one or fewer. In this article, we applied these ideas to develop an enriched perspective of research design for studying CASs. Methodology/Approach: We conducted a theoretical analysis of organizations as CASs, identifying relevant characteristics for research designs. We then explored two ideas from organizational theory and discussed the implications for research designs. Findings: Weick's idea of "design as a verb" helps in understanding dynamic and process-oriented research design. The idea of "learning from samples of one or fewer" of March, Sproull, and Tamuz provides strategies for research design that enables learning from meager evidence. When studying HCOs, research designs are likely to be more effective when they (a) anticipate change, (b) include tension, (c) capitalize on serendipity, and (d) use an "act-then-look" mind set. Implications for practice are discussed. Practice Implications: Practitioners who understand HCOs as CASs will be cautious in accepting findings from studies that treat HCOs mechanistically. They will consider the characteristics of CAS when evaluating the evidence base for practice. Practitioners can use the strategies proposed in this article to stimulate discussion with researchers seeking to conduct research in their HCO.
Family perspectives on communication with healthcare providers during end-of-life cancer care.

PURPOSE/OBJECTIVES To assess healthcare provider communication about end-of-life (EOL) and hospice care with patients with terminal cancer and their families, from the perspective of the family members. DESIGN Exploratory, qualitative study using focus group discussion. SETTING University of Maryland Greenebaum Cancer Center. SAMPLE 24 spouses and first-degree relatives of deceased patients with cancer who had been treated at the cancer center from 2000-2002. METHODS Family members participated in one of two focus group discussions and completed a short questionnaire regarding their sociodemographic characteristics and the type of EOL care their deceased relatives had received. Quantitative data were analyzed using descriptive statistics. Qualitative data were audiotaped and analyzed by comparing, contrasting, and summarizing content themes from the focus groups using NUD IST 5(N5) software. MAIN RESEARCH VARIABLES Family perceptions of communication with the healthcare team in EOL cancer care. FINDINGS Participants associated the information, content, style, language, and timing of communication about EOL and hospice care from healthcare professionals with patient age, attitudes, and compliance with medical decisions. Informed decisions about EOL care by patients and their family members, including the use of hospice services, appeared to be compromised by these types of communication biases. CONCLUSIONS Satisfaction with EOL care was associated with the perceived quality of communication among patients, family members, and the healthcare team. IMPLICATIONS FOR NURSING Study findings highlight the importance of training healthcare professionals in the content, timing, and potential biases associated with information delivery to facilitate informed decisions about EOL and hospice care to dying patients and their families.
The acute phase protein haptoglobin and its relation to oxidative status in piglets undergoing weaning-induced stress

Abstract Haptoglobin (Hp) prevents the hemoglobin driven generation of hydroxyl radicals and lipid peroxides. Hp can reduce the neutrophil respiratory burst and is an antioxidative molecule in its own right. We aimed to evaluate Hp concentrations, oxidative stress and antioxidative capacity in blood during weaning and to characterise potential relationships between these parameters. Two batches of 10 piglets each (2 trials) weaned at the age of 27–30 days were fed a starter feed mix ad libitum. Blood samples were taken 1 week before weaning and at weekly intervals thereafter. Oxidative stress was monitored via the D-ROM® system, antioxidative capacity was measured with the TEAC assay and Hp concentrations were measured by ELISA. Neutrophil phagocytic activity and oxidative burst were examined via flow-cytometry. Body weights were recorded weekly. Hp concentrations were increased in both trials post-weaning (P < 0.01); oxidative stress and oxidative burst were elevated in trial I (P < 0.005). In trial I, Hp and ROM values returned to baseline levels at 6 weeks post-weaning. The piglets in trial II showed respiratory symptoms and maintained elevated Hp concentrations. ROM values and Hp were related (r = 0.58; P < 0.01). Hp and body weight gain were inversely related post-weaning.
Overexpression of KIR inhibitory ligands (HLA-I) determines that immunosurveillance of myeloma depends on diverse and strong NK cell licensing

ABSTRACT Missing self recognition makes cancer sensitive to natural killer cell (NKc) reactivity. However, this model disregards the NKc licensing effect, which highly increases NKc reactivity through interactions of inhibitory killer cell immunoglobulin-like receptors (iKIR) with their cognate HLA-I ligands. The influence of iKIR/HLA-ligand (HLA-C1/C2) licensing interactions on the susceptibility to and progression of plasma cell (PC) dyscrasias was evaluated in 164 Caucasian patients and 286 controls. Compared to controls, myeloma accumulates KIR2DL1−L2+L3− genotypes (2.8% vs. 13.2%, p < 0.01, OR = 5.29) and less diverse peripheral repertoires of NKc clones. Less diverse and weaker-affinity repertoires of iKIR2D/HLA-C licensing interactions increased myeloma susceptibility. Thus, the complete absence of conventional iKIR2D/HLA-C licensing interactions (KIR2DL1−L2+L3−/C2C2, 2.56% vs. 0.35%; p < 0.05; OR = 15.014), single-KIR2DL3+/C1+ (20.51% vs. 10.84%; p < 0.05; OR = 2.795) and single-KIR2DL2+/C1+ (12.82% vs. 4.9%; p < 0.01; OR = 5.18) interactions were over-represented in myeloma, compared to controls. Additionally, KIR2DL1−L2+L3− (20% vs. 83%, p < 0.00001) as well as KIR3DL1− (23% vs. 82%, p < 0.00001) genotypes had a dramatic negative impact on the 3-y progression-free survival (PFS), particularly in patients with low-tumor burden. Remarkably, myeloma-PCs, compared to K562 and other hematological cancers, showed substantial over-expression of HLA-I (“increasing-self” instead of missing-self), including HLA-C, and mild expression of ligands for NKc activating receptors (aRec) CD112, CD155, ULBP-1 and MICA/B, which apparently renders myeloma-PCs susceptible to lysis mainly by licensed NKc. KIR2DL1−L2+L3−/C2C2 patients (with no conventional iKIR2D/HLA-C licensing interactions) lyse K562 but barely lyse myeloma-PCs (4% vs. 15%; p < 0.05, compared to controls). These results support a model where immunosurveillance of no-missing-self cancers, e.g., myeloma, mainly depends on NKc licensing.
Reducing Obesity Stigma via a Brief Documentary Film: A Randomized Trial

The stigma of obesity impacts individuals across numerous life domains, and people with obesity are offered little legal protection against discrimination based on their body type. While a number of experiments have shown that stigmatizing attitudes toward obesity are somewhat malleable, fewer studies have tested the impact of interventions deployable outside of the lab. Fewer still have measured the impact on individuals’ support for equal rights for people with obesity. This randomized trial examined the effects of viewing the weight stigma portion of HBO’s The Weight of the Nation documentary on viewers’ attitudes about obesity across several important domains, including support for equal rights for those with obesity relative to control participants. Participants were 109 young adults who watched a portion of HBO’s The Weight of the Nation documentary or a control video. Following completion of the video, participants were asked to volunteer for a second unrelated study on prejudice in an adjacent computer lab. It was under the guise of this “unrelated study” that weight bias was assessed. Participants’ negative judgments of people with obesity, desire for social distance, and support for equal rights for people with obesity improved after watching the video. Their perceived attractiveness of people with obesity did not change relative to the control condition. This study finds support for the use of a brief documentary film as a means to reduce stigma against persons with obesity.
Femtocell gateway scheduling for capacity and fairness improvement in neighboring femtocell networks

In this paper we analyze various user assignment and scheduling policies for neigbouring femtocell networks. The trade-off between capacity maximization and fairness is investigated and a combined user assignment and proportional fair (PF) scheduling procedure for a femtocell gateway is proposed. The flexibility of the proposed architecture in terms of capacity and fairness is studied via various simulation scenarios. It is shown that by changing parameters in the proposed method one can play-out between fairness and capacity in a femtocell network. In order to decrease the number of the handovers between femtocells, we propose that a femtocell user should be scheduled with the same femtocell base station for a duration of superframe, i.e, cell re-selection should be done in every superframe. The performance of the combined user assignment and PF scheduling scheme is investigated under different superframe considerations and it is shown that a wide range of performance results (in terms of capacity, fairness, handover frequency) could be achieved.
Automated segmentation and quantification of actin stress fibres undergoing experimentally induced changes

The actin cytoskeleton is a main component of cells and it is crucially involved in many physiological processes, e.g. cell motility. Changes in the actin organization can be effected by diseases or vice versa. Due to the nonuniform pattern, it is difficult to quantify reasonable features of the actin cytoskeleton for a significantly high cell number. Here, we present an approach capable to fully segment and analyse the actin cytoskeleton of 2D fluorescence microscopic images with a special focus on stress fibres. The extracted feature data include length, width, orientation and intensity distributions of all traced stress fibres. Our approach combines morphological image processing techniques and a trace algorithm in an iterative manner, classifying the segmentation result with respect to the width of the stress fibres and in nonfibre‐like actin. This approach enables us to capture experimentally induced processes like the condensation or the collapse of the actin cytoskeleton. We successfully applied the algorithm to F‐actin images of cells that were treated with the actin polymerization inhibitor latrunculin A. Furthermore, we verified the robustness of our algorithm by a sensitivity analysis of the parameters, and we benchmarked our algorithm against established methods. In summary, we present a new approach to segment actin stress fibres over time to monitor condensation or collapse processes.