Miracle-dz/UniFAR-FTUs huggingface dataset:
GEM: A Gaussian evolutionary method for predicting protein side‐chain conformations

We have developed an evolutionary approach to predicting protein side‐chain conformations. This approach, referred to as the Gaussian Evolutionary Method (GEM), combines both discrete and continuous global search mechanisms. The former helps speed up convergence by reducing the size of rotamer space, whereas the latter, integrating decreasing‐based Gaussian mutations and self‐adaptive Gaussian mutations, continuously adapts dihedrals to optimal conformations. We tested our approach on 38 proteins ranging in size from 46 to 325 residues and showed that the results were comparable to those using other methods. The average accuracies of our predictions were 80% for χ1, 66% for χ1 + 2, and 1.36 Å for the root mean square deviation of side‐chain positions. We found that if our scoring function was perfect, the prediction accuracy was also essentially perfect. However, perfect prediction could not be achieved if only a discrete search mechanism was applied. These results suggest that GEM is robust and can be used to examine the factors limiting the accuracy of protein side‐chain prediction methods. Furthermore, it can be used to systematically evaluate and thus improve scoring functions.
Regulatory T Cells Suppress T Cell Activation at the Pathologic Site of Human Visceral Leishmaniasis

Suppression of T cell response is thought to be involved in the pathogenesis of visceral leishmaniasis (VL). Regulatory T cell (Treg) mediated immune-suppression is reported in animal models of Leishmania infection. However, their precise role among human patients still requires pathologic validation. The present study is aimed at understanding the frequency dynamics and function of Treg cells in the blood and bone marrow (BM) of VL patients. The study included 42 parasitologically confirmed patients, 17 healthy contact and 9 normal bone marrow specimens (NBM). We show i) the selective accumulation of Treg cells at one of the disease inflicted site(s), the BM, ii) their in vitro expansion in response to LD antigen and iii) persistence after successful chemotherapy. Results indicate that the Treg cells isolated from BM produces IL-10 and may inhibit T cell activation in IL-10 dependent manner. Moreover, we observed significantly higher levels of IL-10 among drug unresponsive patients, suggesting their critical role in suppression of immunity among VL patients. Our results suggest that IL-10 plays an important role in suppression of host immunity in human VL and possibly determines the efficacy of chemotherapy.
A Cognitive Beamforming Scheme for Coexistence of Incumbent and Cognitive Radios

We propose a new cognitive beamforming scheme for coexistence of IR (Incumbent Radio) CR (Cognitive Radio). The proposed cognitive beamforming scheme does not cause any interference to the IRU (IR User), while the CRU (Cognitive Radio User) is served without additional radio resource consumption. Simulation results show that when using the proposed scheme the CRU does not interfere to the IRU and there is little bit error rate performance degradation of the CRU as compared to that of the ideal beamforming system which does not consider the IR priority.
Regulation of asymmetric positioning of nuclei by Wnt and Src signaling and its roles in POP-1/TCF nuclear asymmetry in Caenorhabditis elegans

In various polarized cells, positions of nuclei are often off‐center. However, extrinsic signals regulating nuclear off‐centering and its biologic roles remain to be elucidated. In Caenorhabditis elegans, polarity of the EMS cell undergoing asymmetric division is regulated by the MOM‐2/Wnt and MES‐1 signals from its posterior neighbor P2 cell. We show that after divisions of different cells including EMS, the nuclei of the posterior but not anterior daughter cells are anchored to the posterior cell cortex via centrosomes. We also show that this nuclear anchoring is regulated by components of the Wnt pathway and SRC‐1 that functions in MES‐1 signaling. To understand the biologic roles of nuclear anchoring, we analyzed its effects on asymmetric nuclear localization of POP‐1/TCF that is also regulated by Wnt and Src signaling. We found that in mom‐2 mutants where the nuclear anchoring and POP‐1 asymmetry is partially inhibited, the proximity of the nucleus to the cell cortex correlated with POP‐1 asymmetry. Furthermore, in mutants of mom‐2, the defect in the anchoring is clearly correlated with that of asymmetric fate determination. These results suggest that the asymmetric nuclear anchoring functions in asymmetric division by enhancing POP‐1 asymmetry.
ILP-based co-optimization of cut mask layout, dummy fill, and timing for sub-14nm BEOL technology

Self-aligned multiple patterning (SAMP), due to its low overlay error, has emerged as the leading option for 1D gridded back-end-of-line (BEOL) in sub-14nm nodes. To form actual routing patterns from a uniform "sea of wires", a cut mask is needed for line-end cutting or realization of space between routing segments. Constraints on cut shapes and minimum cut spacing result in end-of-line (EOL) extensions and non-functional (i.e. dummy fill) patterns; the resulting capacitance and timing changes must be consistent with signoff performance analyses and their impacts should be minimized. In this work, we address the co-optimization of cut mask layout, dummy fill, and design timing for sub-14nm BEOL design. Our central contribution is an optimizer based on integer linear programming (ILP) to minimize the timing impact due to EOL extensions, considering (i) minimum cut spacing arising in sub-14nm nodes; (ii) cut assignment to different cut masks (color assignment); and (iii) the eligibility to merge two unit-size cuts into a bigger cut. We also propose a heuristic approach to remove dummy fills after the ILP-based optimization by extending the usage of cut masks. Our heuristic can improve critical path performance under minimum metal density and mask density constraints. In our experiments, we study the impact of number of cut masks, minimum cut spacing and metal density under various constraints. Our studies of optimized cut mask solutions in these varying contexts give new insight into the tradeoff of performance and cost that is afforded by cut mask patterning technology options.
The asthma–COPD overlap syndrome: do we really need another syndrome in the already complex matrix of airway disease?

The term asthma–COPD overlap syndrome (ACOS) is one of multiple terms used to describe patients with characteristics of both COPD and asthma, representing ~20% of patients with obstructive airway diseases. The recognition of both sets of morbidities in patients is important to guide practical treatment decisions. It is widely recognized that patients with COPD and coexisting asthma present with a higher disease burden, despite the conceptual expectation that the “reversible” or “treatable” component of asthma would allow for more effective management and better outcomes. However, subcategorization into terms such as ACOS is complicated by the vast spectrum of heterogeneity that is encapsulated by asthma and COPD, resulting in different clinical clusters. In this review, we discuss the possibility that these different clusters are suboptimally described by the umbrella term “ACOS”, as this additional categorization may lead to clinical confusion and potential inappropriate use of resources. We suggest that a more clinically relevant approach would be to recognize the extreme variability and the numerous phenotypes encompassed within obstructive airway diseases, with various degrees of overlapping in individual patients. In addition, we discuss some of the evidence to be considered when making practical decisions on the treatment of patients with overlapping characteristics between COPD and asthma, as well as the potential options for phenotype and biomarker-driven management of airway disease with the aim of providing more personalized treatment for patients. Finally, we highlight the need for more evidence in patients with overlapping disease characteristics and to facilitate better characterization of potential treatment responders.
Comparison between access selection algorithms in multi-operator wireless networks

In fifth generation mobile network, Radio Access Network sharing is an attractive solution for operators to counter the traffic growth and build cost-effective networks in order to improve coverage and capacity at reasonable investments and operational costs. It consists of sharing radio access resources between two or more operators. In such multi-operator environment access selection decision is an important issue for the mobile user and his home operator which the user has contract with. In literature, the majority of access selection algorithms are based on game theory which is very complex for implementation and the decision is slower in comparison with Multiple Attributes Decision Making (MADM) methods. In this paper, we apply Simple Additive Weighting (SAW) methods and Nearest Performance Handover (NPH) algorithm for the access selection in a multi-operator environment. These algorithms based on MADM were initially conceived for the selection decision in a single operator environment. In addition, we compare the performance of these algorithms with our previously proposed cost function for the access selection in a multi-operator sharing network. Performance analyses are made in terms of user blocking percentages and global achieved profit. Simulation results showed that our decision algorithm guarantee the lowest blocking probability for all operators, it prevents overloading operator's with high numbers of guest users which affect own clients acceptance. In addition, it improves global achieved profits for all cooperating operators. However, SAW methods showed better performance than NPH concerning users blocking percentages, but NPH guarantees higher profits than SAW methods for the operators with limited capacity.
Estimation of the Vibration Decrement of an Offshore Wind Turbine Support Structure Caused by its Interaction with Soil

In today’s cutting costs environment in the offshore wind industry, significant achievements can be made with a better assessment of dynamic soil-pile interaction. More knowledge regarding the contribution of the dynamic soil-pile interaction to damping of an offshore wind turbine structure (OWT) could perceptibly reduce the fabrication costs of an OWT. Currently, not much is known about the contribution of soil to the total damping of the vibration of an OWT which consists of five main damping mechanisms: aerodynamic-, hydrodynamic-, structural-, soil- and a passive sloshing damper in the nacelle. The values for this contribution applied in the industry today - mostly calculated analogously to a study performed in 1980 by M.F. Cook - can be expected to be on the low side (conservative), and it is acknowledged that it might be higher. More research on the topic is recommended. Increased damping of the vibrations of an OWT decreases the occurring stresses in the structure which in turn results in lower (often design driving) fatigue damage accumulation. Presence of more damping than currently assumed would justify either designing more light-weight structures using less construction steel, or allowing for longer (insured) OWT lifetimes than the currently applied 20 years. Both measures significantly reduce costs of offshore generated wind power. This research evaluates measured signals of twelve ’rotor stop’ - tests on an offshore wind turbine at the Dong Energy owned - Burbo Bank wind farm in the Irish Sea. The recorded data comprises the vibration decay of the structure, measured with an accelerometer and strain gauges along the tower. An analytical model has been developed enabling analyses of the origin of the measured signals. Two main frequencies were identified in the measurements and, using the different measurement locations and the model, the corresponding modal shapes were identified. A crucial distinction between the two modal shapes is the difference in motion of the lower part of the structure. The amplitudes of displacement and velocity at this location are much smaller for the second observed modal shape than for the first. A large difference in damping ratio between the two frequencies was identified. The difference in damping is attributed to the different effect the soil can have on the damping of these two frequencies. This can be explained by the varying amplitudes of their modes in the soil embedded part of the structure. The measured total damping (19 % logarithmic decrement which is 3 % ratio of critical) for the first natural bending frequency of the tower, and the possible order of magnitude of the found contribution of soil on this damping (~ 9.5 % log. decr. or 1.5 % ratio) of this particular OWT is significantly larger than the order of magnitude used in the industry today (respectively ~ 2.5 % log. decr. and ~0.44 %).
Lifetime maternal experiences of abuse and risk of pre-natal depression in two demographically distinct populations in Boston.

BACKGROUND To investigate lifetime history of interpersonal abuse and risk of pre-natal depression in socio-economically distinct populations in the same city. METHODS We examined associations of physical and sexual abuse with the risk of pre-natal depression in two cohorts in the Boston area, including 2128 participants recruited from a large urban- and suburban-managed care organization (Project Viva) and 1509 participants recruited primarily from urban community health centres (Project ACCESS). Protocols for the studies were designed in parallel to allow us to merge data to enhance ethnic and socio-economic diversity in the combined sample. In mid-pregnancy, the Personal Safety Questionnaire and Edinburgh Postnatal Depression Scale (EPDS) were administered in both cohorts. An EPDS score ≥ 13 indicated probable pre-natal depression. Logistic regression was used to estimate the odds ratio (OR) of pre-natal depression associated with lifetime abuse history. RESULTS Project ACCESS participants were twice as likely as Project Viva participants to report symptoms consistent with pre-natal depression: 22% of Project ACCESS participants had EPDS scores ≥ 13, compared with 11% of Project Viva participants. Fifty-seven percent of women in ACCESS and 46% in Viva reported lifetime physical and/or sexual abuse. In merged analysis, women reporting lifetime physical or sexual abuse had an OR for mid-pregnancy depression of 1.63 [95% confidence interval (95% CI): 1.29-2.07], adjusted for age and race/ethnicity. Lifetime histories of physical abuse [OR 1.48 (95% CI 1.15-1.90)] and sexual abuse [OR 1.68 (95% CI 1.24-2.28)] were independently associated with pre-natal depression. When child/teen, pre-pregnancy adult and pregnancy life periods were considered simultaneously, abuse in childhood was independently associated with an OR of 1.23 (95% CI 1.00-1.59), pre-pregnancy adult abuse with an OR of 1.70 (95% CI 1.31-2.21) and abuse during pregnancy with an OR of 1.77 (95% CI 1.14-2.74). Further adjustment for childhood socio-economic position made no material difference, and there were no clear interactions between abuse and adult socio-economic position. CONCLUSIONS Physical and sexual abuse histories were positively associated with pre-natal depression in two economically and ethnically distinct populations. Stronger associations with recent abuse may indicate that the association of abuse with depression wanes with time or may result from less accurate recall of remote events.
Relationship between self-care and depression and anxiety symptoms in individuals undergoing hemodialysis

Objective: to evaluating the ability for self-care and its relationship with depression and anxiety symptoms in hemodialysis patients. Methods: a correlational, cross-sectional study conducted with 100 participants. The following instruments were used: Appraisal of Self Care Agency Scale – Revised (ASAS-R), which indicates the ability of patients to self-care, and the Hospital Anxiety and Depression Scale, which evaluates the presence or absence of depression and anxiety symptoms. Results: the participants had a mean score of 60.64 (±8.24) on the Appraisal of Self Care Agency Scale - Revised, indicating a good level of self-care agency. A negative correlation of moderate magnitude was found between the ability to self-care and symptoms of anxiety (r=-0.328) and depression (r=-0.387). Conclusion: individuals undergoing hemodialysis treatment presented good self-care agency and those with depression and/or anxiety symptoms showed less ability to self-care.
The Emergence of Sustainability as the New Dominant Logic: Implications for Information Systems

A dominant logic describes the manner is which a firm or society organizes much of its activity in order to be successful. Historical analysis indicates that the information systems developed during a period reflect the needs of the current dominant logic of that era. It is argued that the current customer service dominant logic is being replaced or complemented by a sustainability dominant logic, which reflects the growing concern with environmental issues. The implications for IS scholarship and education are discussed. In particular, there will likely be a greater emphasis on optimization and simulation techniques and more attention to managing large data sets in research and teaching. In addition, there is a need to revisit socio-technical frameworks that ignore the environment as a key factor in IS design and deployment decisions.
Intensity of vocal responses to spider and snake pictures in fearful individuals

Objective Strong bodily responses have repeatedly been shown in participants fearful of spiders and snakes when they see pictures of the feared animal. In this study, we investigate if these fear responses affect voice intensity, require awareness of the pictorial stimuli, and whether the responses run their course once initiated. Method Animal fearful participants responded to arrowhead‐shaped probes superimposed on animal pictures (snake, spider, or rabbit), presented either backwardly masked or with no masking. Their task was to say ‘up’ or ‘down’ as quickly as possible depending on the orientation of the arrowhead. Arrowhead probes were presented at two different stimulus onset asynchronies (SOA), 261 or 561-ms after picture onset. In addition to vocal responses, electrocardiogram, and skin conductance (SC) were recorded. Results No fear‐specific effects emerged to masked stimuli, thereby providing no support for the notion that fear responses can be triggered by stimuli presented outside awareness. For the unmasked pictures, voice intensity was stronger and SC response amplitude was larger to probes superimposed on the feared animal than other animals, at both SOAs. Heart rate changes were greater during exposure to feared animals when probed at 561-ms, but not at 261-ms, which indicates that a fear response can change its course after initiation. Conclusion Exposure to pictures of the feared animal increased voice intensity. No support was found for responses without awareness. Observed effects on heart rate may be due to change in parasympathetic activation during fear response.
The temporal association of excessive health expenditure with suicidal ideation among primary income earners: a cross-sectional design using the Korean Welfare Panel Survey (KoWePS)

Objective Excessive health expenditure (EHE) is a global issue for households suffering from high-cost medical conditions, low incomes and limited insurance coverage. After the international financial crisis of 2008, EHE became a social problem in developed countries. Such economic crisis might induce severe mental stress, resulting in suicidal ideation. Methods We used the Korean Welfare Panel Study (KoWePS) from 2011 to 2013 and selected primary income earners, who were defined as practical and economic representatives of households; the total number of analysed samples was 4247 of 5717 households in the database. We only included households that had never experienced EHE before 2011. To examine the temporal relationship between EHE and suicidal ideation, we conducted a logistic regression analysis. Results Among 4247 participants, 146 (3.4%) experienced suicidal ideation, whereas 4101 (96.6%) did not. One scale of depression score (OR=1.28, CI 1.23 to 1.34, p<0.001) was associated with increased suicidal ideation. Such ideation was influenced to a greater extent by a recent EHE above 10% of disposable income (OR=1.91, CI 1.16 to 3.15, p=0.012) than by either a remote EHE (OR=1.29, CI 0.71 to 2.32) or one in 2011 and 2012 (OR=1.67, CI 1.01 to 2.78, p=0.048). Conclusions In this study, more recent EHE resulted in more suicidal ideation. In conclusion, we suggest that recent household EHE might be considered as an important factor to prevent suicidal ideation and to improve the mental health of individuals.
Maximum-density droplet and charge redistributions in quantum dots at high magnetic fields

We have measured electron transport through a vertical quantum dot containing a tunable number (between 0 and 40) of electrons. Over a region of the magnetic field the electrons are spin polarized and occupy successive angular momentum states. This is the maximum-density-droplet ( MDD) state. The stability region where the MDD is the ground state decreases for increasing electron number. The instability of the MDD and other transitions in this high B region are accompanied by a redistribution of charge which abruptly changes the area of the electron droplet. [S0031-9007(99)08873-0] PACS numbers: 73.20. Dx, 71.45. Gm, 73.40. Hm In this Letter we study quantum dots [1,2] in the quantum Hall regime and exploit the fact that dots contain a tunable and well-defined number of electrons. In particular, we consider the spin-polarized, maximumdensity-droplet ( MDD) state at high magnetic fields that corresponds to filling factor n › 1 in a large two dimensional electron gas. The stability of this state is set by a balance of forces [3‐6] acting on this finite electron system, namely, the inward force of the confining potential, the repulsive force of the direct Coulomb interaction between electrons, and a binding force due to the exchange interaction. In addition, Zeeman energy and correlation effects are important. As the magnetic field and the electron number are changed, the relative strengths of these forces are tuned, which induces transitions between the MDD and other states. Earlier these transitions were measured in the linear response regime [1,7]. We report detailed measurements in linear and nonlinear transport showing that the transitions are accompanied by a significant redistribution of chargein this many-body system. Our vertical quantum dot is made from a double barrier resonant tunneling structure with an InGaAs well, AlGaAs barriers, and n-doped GaAs source and drain contacts [8]. The device is processed in the shape of a submicron circular pillar with a diameter of 0.54 mm, and a self-aligned gate surrounds it. We discuss data taken on one particular device, but comparable results have been obtained on several devices. A magnetic field, B, is applied perpendicular to the plane in which the electrons are confined. The energy spectrum of the quantum dot is derived from transport experiments at a temperature of 100 mK in the Coulomb blockade regime. A dc source-drain voltage, VSD, is applied and the current, I, is measured versus gate