Miracle-dz/UniFAR-FTUs huggingface dataset:
PROMALS3D: a tool for multiple protein sequence and structure alignments

Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structures is a valuable source to improve alignment quality. We explore the use of 3D structural information to guide sequence alignments constructed by our MSA program PROMALS. The resulting tool, PROMALS3D, automatically identifies homologs with known 3D structures for the input sequences, derives structural constraints through structure-based alignments and combines them with sequence constraints to construct consistency-based multiple sequence alignments. The output is a consensus alignment that brings together sequence and structural information about input proteins and their homologs. PROMALS3D can also align sequences of multiple input structures, with the output representing a multiple structure-based alignment refined in combination with sequence constraints. The advantage of PROMALS3D is that it gives researchers an easy way to produce high-quality alignments consistent with both sequences and structures of proteins. PROMALS3D outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods.
Time to Change – Let's End Mental Health Discrimination: the Challenges Ahead

October 2007 marked the launch of another programme in England to tackle stigma and discrimination. 'Time to Change' models national initiatives from New Zealand and Scotland drawing on an expanding stigma evidence base 1 as well as lessons from past projects, including the Royal College of Psychiatrists' 'Defeat Depression' and 'Changing Minds' campaigns. How might this programme succeed where others have stalled? The programme is resource rich with £18 million from the Big Lottery Fund and Comic Relief to channel into 35 linked programmes. It has 4 years to prove change among targeted audiences within a 30 million adult reach. It is a four-party coalition with a desire to learn from organisations across health and disability fields. It is adopting an evidence-based approach 2 – national social marketing, service user leadership and engagement , local direct action, multiple targets using 'stick and carrot' approaches – but this does not guarantee success. Key challenges are identifiable. Preparatory consultation during February 2008 using a pragmatic, non-systematic survey method through the membership networks of 18 organisations generated responses from 3038 service users and 661 family or friend carers. This consultation emphasised first, that stigma and discrimination are widespread and their impact far-reaching. (a) Seventy-one per cent reported to have stopped doing things – accessing employment, making friends, joining groups, engaging with health professionals. (b) Seventy-three per cent reported anticipated discrimination including one in two who fear disclosing their health problems because of the negative reactions they might receive. (c) Carers reported fewer personal effects but 85% felt that the person they supported was affected. (d) Time to Change will need to target its efforts to have a meaningful impact in any one area. Second, that combating stigma and discrimination is not straightforward. Service users and carers warned that the entangled nature of mental illness and their own and other people's reactions make generic solutions difficult to find. Pinpointing exact goals for the 35 Time to Change programmes in terms of what needs to change will be central to proving any success. Third, that Time to Change must set realistic goals. Variation in experiences particularly relating to physical health disabilities, sexuality, severe mental illness diagnosis and ethnicity of carers were found. Stakeholders will not equally benefit from Time to Change and the programme must be open and honest about its limitations from the outset. There is a danger that if it 'fails' to have …
Identification of the Chemokine CX3CL1 as a New Regulator of Malignant Cell Proliferation in Epithelial Ovarian Cancer

Background Little is known about the molecules that contribute to the growth of epithelial ovarian carcinomas (EOC), which remain the most lethal gynecological cancer in women. The chemokine Fractalkine/CX3CL1 has been widely reported to play a biologically relevant role in tumor growth and spread. We report here the first investigation of the expression and role of CX3CL1 in EOC. Results Epithelial cells from the surface of the ovary and the Fallopian tubes and from benign, borderline and malignant tumors all stained positive for CX3CL1. In tumor specimens from 54 women who underwent surgical treatment for EOC diagnosis, CX3CL1 immunoreactivity was unevenly distributed in epithelial tumor cells, and ranged from strong (33%) to absent (17%). This uneven distribution of CX3CL1 did not reflect the morphological heterogeneity of EOC. It was positively correlated with the proliferation index Ki-67 and with GILZ (glucocorticoid-induced leucine zipper), previously identified as an activator of the proliferation of malignant EOC cells. Hierarchical clustering analysis, including age at diagnosis, tumor grade, FIGO stage, Ki-67 index, CX3CL1, SDF-1/CXCL12 and GILZ immunostaining scores, distinguished two major clusters corresponding to low and high levels of proliferation and differing in terms of GILZ and CX3CL1 expression. GILZ overexpression in the carcinoma-derived BG1 cell line resulted in parallel changes in CX3CL1 products. Conversely, CX3CL1 promoted through its binding to CX3CR1 AKT activation and proliferation in BG1 cells. In a mouse subcutaneous xenograft model, the overexpression of GILZ was associated with higher expression of CX3CL1 and faster tumor growth. Conclusion Our findings highlight the previously unappreciated constitutive expression of CX3CL1 preceding tumorigenesis in ovarian epithelial cells. Together with GILZ, this chemokine emerges as a regulator of cell proliferation, which may be of potential clinical relevance for the selection of the most appropriate treatment for EOC patients.
Exploring Recovery from Operating System Lockups

Operating system lockup errors can render a computer unusable by preventing the execution other programs. Watchdog timers can be used to recover from a lockup by resetting the processor and rebooting the system when a lockup is detected. This results in a loss of unsaved data in running programs. Based on the observation that volatile memory is not affected when a processor a reset occurs, we present an approach to recover from a watchdog reset with minimal or zero loss of application state. We study the resolution of lockup conditions using thread termination and using exception dispatch. Thread termination can still result in a usable system and is already used as a recovery strategy for other errors in Linux. Using exceptions allows developers to write code to handle a lockup within the erroneous thread and attempt application transparent recovery. Fault injection experiments show that a significant percentage of lockups can be recovered by thread termination. Exception handling further improves the recoverability of the operating system.
On the Performance of Hybrid Digital-Analog Coding for Broadcasting Correlated Gaussian Sources

We consider the problem of sending a bivariate Gaussian source S=(S1,S2) across a power-limited two-user Gaussian broadcast channel. User i (i=1,2) observes the transmitted signal corrupted by Gaussian noise with power σi2 and desires to estimate Si. We study hybrid digital-analog (HDA) joint source-channel coding schemes and analyze the region of (squared-error) distortion pairs that are simultaneously achievable. Two cases are considered: 1) broadcasting with bandwidth compression, and 2) broadcasting with bandwidth expansion. We modify and adapt HDA schemes of Wilson et al. and Prabhakaran et al. , originally proposed for broadcasting a single common Gaussian source, in order to provide achievable distortion regions for broadcasting correlated Gaussian sources. For comparison, we also extend the outer bound of Soundararajan et al. from the matched source-channel bandwidth case to the bandwidth mismatch case.
A Transparent Failover Mechanism for a Mobile Network with Multiple Mobile Routers

In a mobile network that is multihomed by multiple mobile routers, a mobile router that loses link connectivity can be replaced by the other mobile routers. We propose a transparent failover mechanism (TFM) to provide seamless Internet services to nodes in the mobile network, which is validated by implementing a real test-bed. Compared to the network mobility basic support protocol, TFM does not require the nodes attached to the failed mobile router to change their addresses, and hence has two advantages: (a) IP connectivity is maintained transparently, and (b) failover is quickly accomplished by avoiding the address re-configuration process in each node.
Reinforcement Learning Control for Biped Robot Walking on Uneven Surfaces

Biped robots based on the concept of (passive) dynamic walking are far simpler than the traditional fullyI controlled walking robots, while achieving a more natural gait and consuming less energy. However, lightly actuated dynamic walking robots, which rely on the natural limit cycle of their mechanical structure, are very sensitive to ground disturbances. Already a very small step down can cause the robot to lose stability. In this paper, we investigate the use of reinforcement learning to make a dynamic walking robot more robust against ground disturbances. The learning controller is applied to a simulated two-link biped which is an abstraction of a mechanical prototype developed at the Delft Biorobotics Laboratory. The learning controller has been designed such that it can be applied as a straightforward extension of the proportionalI-derivative (PD) controller currently used to drive the robot's pneumatic actuators. The learning controller is therefore suitable for the future implementation in the robot hardware. Simulation results demonstrate that the biped quickly learns to overcome step-down disturbances on the floor up to 10% of the leg length, without compromising the natural walking style provided by the PD controller, which was optimized for walking on an even surface.
R 20 HIGH-SPEED GENERAL PURPOSE DEMODULATION PIXELS BASED ON BURIED PHOTODIODES

Using a standard 0.18um CMOS process with a buried photodiode (BPD) option, test pixels with a single transfer gate were characterized. The test pixels enabled finding an optimized BPD layout that minimizes the potential barriers hindering the charge transfer. Demodulation pixels having a 6.3um pitch or less were then developed and demonstrated to demodulate light signals up to at least 50MHz. Moreover, charge transfer noise was highly reduced by optimizing the pixel operating conditions. Demodulation of single photoelectrons could thus be made possible.
USING HIGH Mg-CONTENT CORED-WIRE TO SPHEROIDIZE AND DESULPHURIZE DUCTILE IRON MELT IN INDUSTRIAL EXPERIMENTS

40% Mg-content cored-wire was used to desulphurize and spheroidize ductile iron melt in industrial experiments. The optimal feeding speed and suitable treatment temperature were determined in the experiments. And cored-wire method and pouring method were compared.Conclusions have been drawn that, under these conditions in the experiments, the optimal feeding speed is 15m/min, treatment temperature should be as low as possible, 1400-1450℃ generally; and cored-wire method can act more effective in ductile iron melt desulphurization and spheroid than pouring method.
Flotation Research on Cuprite-Type Oxide Copper in XinJiang

Low-grade oxide copper ore is an important resource, reserves of which are scattered all over the world. In the present study, the characteristics of oxide copper ore are studied using multi-element analysis and X-ray diffraction. The oxide copper minerals in the ore are mainly in the form of cuprite, malachite, chrysocollite and azurite. The effects of grinding fineness and agent regulation on flotation are also investigated. Floatability was unsatisfactory because of the many kinds of oxide copper minerals present in the sample. The flotation results indicate that a concentrate grade of 18.32% at 73.46% recovery can be obtained using the closed circuit process of one-stage roughing, three-stage scavenging and two-stage cleaning flotation under the optimum parameters, with raw ore characteristics of 1.29% Cu, 92.25% copper oxidation rate, and 65.59% slime content.
Pleural drainage and pleurodesis: implementation of guidelines in four hospitals

The aim of the present study was to evaluate the implementation of the 2003 Dutch guideline on the diagnosis and treatment of malignant pleural effusions, and the potential effect of the implementation on the clinical outcome of pleurodesis. All patients with malignant pleural effusion who had a pleural drain placed with the intention of performing pleurodesis were registered prospectively in four centres. Details of the procedure and fluid recurrence and survival data were noted. Patients with a proven malignancy (n = 100) were entered into the registration database. Diagnostic guideline recommendations were followed in 60–70% of the patients. Surprisingly, pleurodesis was performed in only 75% of the patients, mainly due to the presence of a trapped lung. All pleurodeses were performed using talc, according to the guideline. Follow-up revealed fluid recurrence in 27 (36%) patients after a mean follow-up of 17 days (range 2–285 days); 14 patients with successful pleurodesis died with a median survival of 61 days (range 13–174 days). Systemic treatment following pleurodesis and good apposition of the pleural surfaces during drainage were good prognostic factors. Despite reasonable-to-good adherence to the guideline, the number of successful pleurodeses was low. Better predictors of a good pleurodesis outcome are needed.
The crystal structure of 1,5-dibenzyl-1H-pyrazolo[3,4-d]pyrimidine-4(5H)-thione

In the title compound, C19H16N4S, the pyrazolo[3,4-d]pyrimidine ring is close to being planar, with the greatest deviation from the mean plane being 0.023 (2) Å for the C atom bearing the thione S atom. The two phenyl rings are nearly perpendicular to the fused ring system [dihedral angles = 71.4 (2) and 78.1 (2)°], but are oriented in opposite directions; the dihedral angle between the phenyl rings is 32.22 (16)°. In the crystal, linear supramolecular chains along [101] are sustained by C—H⋯S interactions.
Analysis of optical waveguide structure using beam propagation method for optical wireless communications

Radiation scattered from a parabolic index planar waveguide with the insertion of metal strip at the centre is analyzed to design the photonic antenna, which transfers the energy from waveguide to free space, using beam propagation method (BPM). This technique allows the interpretation of the metal strip as scattering element of the underlying waveguide mode and radiating sources for the diffracted fields. The parabolic index planar waveguide with the insertion of metal strip with high refractive index value is evaluated and often explicit formulas for the radiating parameters of photonic antennas. The framework allows separation of the effects of the metal strip insertion with high refractive index value and the effects of the specific size of the metal strip element. A straightforward analogy between the effects of the metal strip element's refractive index value, shape and the behaviour of photonic antenna systems allow a clear and sensitive understanding of the effects of metal strip on the directionality of waveguide coupled radiation. The results covered only TE modes and it is possible to achieve high directional photonic antennas in the range of optical wireless frequencies. The results are obtained for various operating wavelengths of parabolic index waveguide structure with power distribution along z-direction and the efficient wavelength is proposed for photonic antenna
Robust classification of rare queries using web knowledge

We propose a methodology for building a practical robust query classification system that can identify thousands of query classes with reasonable accuracy, while dealing in real-time with the query volume of a commercial web search engine. We use a blind feedback technique: given a query, we determine its topic by classifying the web search results retrieved by the query. Motivated by the needs of search advertising, we primarily focus on rare queries, which are the hardest from the point of view of machine learning, yet in aggregation account for a considerable fraction of search engine traffic. Empirical evaluation confirms that our methodology yields a considerably higher classification accuracy than previously reported. We believe that the proposed methodology will lead to better matching of online ads to rare queries and overall to a better user experience.
WERD: Using social text spelling variants for evaluating dialectal speech recognition

We study the problem of evaluating automatic speech recognition (ASR) systems that target dialectal speech input. A major challenge in this case is that the orthography of dialects is typically not standardized. From an ASR evaluation perspective, this means that there is no clear gold standard for the expected output, and several possible outputs could be considered correct according to different human annotators, which makes standard word error rate (WER) inadequate as an evaluation metric. Such a situation is typical for machine translation (MT), and thus we borrow ideas from an MT evaluation metric, namely TERp, an extension of translation error rate which is closely-related to WER. In particular, in the process of comparing a hypothesis to a reference, we make use of spelling variants for words and phrases, which we mine from Twitter in an unsupervised fashion. Our experiments with evaluating ASR output for Egyptian Arabic, and further manual analysis, show that the resulting WERd (i.e., WER for dialects) metric, a variant of TERp, is more adequate than WER for evaluating dialectal ASR.
Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort

This paper presents our approach to retargeting the information retrieval systems designed and/or optimized for retrieval of MEDLINE citations to the task of finding relevant passages in the text of scientific articles. To continue using our TREC 2005 fusion approach, we needed a common representation for the full text biomedical articles to be shared by the four base systems (Essie, SMART, EasyIR and Theme.) The base systems relied upon previously developed NLP, statistical and ML methods. The fusion of the automatic runs improved the results of three contributing base systems at 99.9% significance level on all metrics: document, passage, and aspect precision. The fusion run outperformed Essie, the best of the base systems, at 94% to 99% significance level, with the exception of passage precision. The novelty of the task and the lack of training data inspired our exploration of an interactive approach. The prohibitive cost (in time and domain expert effort) required for a truly interactive retrieval led to a team interaction with one of the base systems – Essie. The initial queries were developed by a computational biologist and a medical librarian. The librarian merged and then refined the queries upon inspecting the initial search results. The refined queries were submitted as a batch without further interaction with the system. The interactive results, the best we achieved, improved over the baseline automatic Essie run at the 91% significance level. The difference between the fusion and the interactive results is not statistically significant.
Far infrared pedestrian detection and tracking for night driving

SUMMARY This paper presents a module for pedestrian detection from a moving vehicle in low-light conditions. The algorithm make use of a single far infrared camera based on a microbolometer. Images of the area ahead of the vehicle are analyzed to determine if any pedestrian might be in its trajectory. Detection is achieved by searching for distributions of temperatures in the scene similar to that of the human body. Those areas with an appropriate temperature, size, and position in the image are classified, by means of a correlation between them and some probabilistic models, which represents the average temperature of the different parts of the human body. Finally, those pedestrians found are tracked in a subsequent step, using an unscented Kalman filter. This final stage of the algorithm enables the algorithm to predict the trajectory of the pedestrian, in a way that does not depend on the movement of the camera. The aim of this system is to warn the vehicle's driver and reduce the reaction time in case an emergency break is necessary.
Adhesion of Annexin 7 Deficient Erythrocytes to Endothelial Cells

Annexin 7 deficiency has previously been shown to foster suicidal death of erythrocytes or eryptosis, which is triggered by increase of intracellular Ca2+ concentration ([Ca2+]i) and characterized by cell shrinkage and cell membrane scrambling with subsequent phosphatidylserine exposure at the cell surface. Eryptosis following increase of [Ca2+]i by Ca2+ ionophore ionomycin, osmotic shock or energy depletion was more pronounced in erythrocytes from annexinA7-deficient mice (anxA7−/−) than in erythrocytes from wild type mice (anxA7+/+). As phosphatidylserine exposure is considered to mediate adhesion of erythrocytes to the vascular wall, the present study explored adhesion of erythrocytes from anx7−/− and anx7+/+-mice following increase of [Ca2+]i by Ca2+ ionophore ionomycin (1 µM for 30 min), hyperosmotic shock (addition of 550 mM sucrose for 2 hours) or energy depletion (removal of glucose for 12 hours). Phosphatidylserine exposing erythrocytes were identified by annexin V binding, cell volume estimated from forward scatter in FACS analysis and adhesion to human umbilical vein endothelial cells (HUVEC) utilizing a flow chamber. As a result, ionomycin, sucrose addition and glucose removal all triggered phosphatidylserine-exposure, decreased forward scatter and enhanced adhesion of erythrocytes to human umbilical vein endothelial cells (HUVEC), effects significantly more pronounced in anx7−/− than in anx7+/+-erythrocytes. Following ischemia, morphological renal injury was significantly higher in anx7−/− than in anx7+/+-mice. The present observations demonstrate that enhanced eryptosis of annexin7 deficient cells is paralleled by increased adhesion of erythrocytes to the vascular wall, an effect, which may impact on microcirculation during ischemia.
Random Walk Features for Network-aware Topic Models

Topic Models such as Latent Dirichlet Allocation (LDA) have been successfully applied as a data analysis and dimensionality reduction tool. With the emergence of social networks, many datasets are available in the form of a network with typed nodes (documents, authors, URLs, publication dates, . . . ) and edges (authorship, citation, friendship, . . . ). We propose a network-aware topic model that integrates rich, heterogeneous, network-based information, representing them using pathtyped random walks. In more detail, the proposed model is based on Dirichlet multinomial regression, an extension of LDA, as well as on random walks for exploiting network information; each document node is characterized by its connectivity to other nodes in the graph through a given set of random walks. A set of sparse latent parameters relate this characterization to topic assignments. Being sparse, the latent parameters give insight into the effect of different network features on the extracted topics.