Miracle-dz/UniFAR-FTUs huggingface dataset:
Human aging and disease: Lessons from age-related macular degeneration

Aging is the most significant risk factor associated with chronic disease in humans. The accumulation of genetic damage throughout life leads to a variety of biological aberrations, including disrupted protein homeostasis, metabolic dysfunction, and altered cellular signaling. Such changes ultimately result in cellular senescence, death, or transformation to uncontrolled proliferation, thereby compromising human health. Events contributing to age-dependent physiological decline also occur in the context of hormonal and metabolic changes, affecting interconnected cellular networks. This complexity often confounds the development of effective treatments for aging and age-related diseases. In contrast to monotherapy and polypharmacology, an innovative systems pharmacology approach can identify synergistic combinations of drugs that modulate distinct mechanistic nodes within a network, minimizing off-target side effects and enabling better therapeutic outcomes. G protein-coupled receptors (GPCRs) are particularly good targets for the application of systems pharmacology, because they activate different signal transduction pathways that can culminate in a common response. Here, we describe a systems pharmacology strategy for the treatment of age-related macular degeneration (AMD), a multifactorial chronic disease of the eye. By considering the retina as part of a large, interconnected network, systems pharmacology will enable the identification of combination therapies targeting GPCRs to help restore genomic, proteomic, and endocrine homeostasis. Such an approach can be advantageous in providing drug regimens for the treatment of AMD, while also having broader ramifications for ameliorating adverse effects of chronic, age-related disease in humans.
Amygdala reactivity in ethnic minorities and its relationship to the social environment: an fMRI study

Abstract Background Ethnic minority individuals have an increased risk of developing a psychotic disorder, particularly if they live in areas of ethnic segregation, or low own group ethnic density. The neurobiological mechanisms underlying this ethnic minority associated risk are unknown. We used functional MRI to investigate neural responses to faces of different ethnicity, in individuals of black ethnicity, and a control group of white British ethnicity individuals. Methods In total 20 individuals of black ethnicity, and 22 individuals of white British ethnicity underwent a 3T MRI scan while viewing faces of black and white ethnicity. Own group ethnic density was calculated from the 2011 census. Neighbourhood segregation was quantified using the Index of Dissimilarity method. Results At the within-group level, both groups showed greater right amygdala activation to outgroup faces. Between groups, the black ethnicity group showed greater right amygdala activation to white faces, compared to the white ethnicity group. Within the black ethnicity group, individuals living in areas of lower own group ethnic density showed greater right amygdala reactivity to white faces (r = −0.61, p = 0.01). Conclusions This is the first time an increased amygdala response to white faces has been demonstrated in individuals of black ethnicity. In the black ethnicity group, correlations were observed between amygdala response and neighbourhood variables associated with increased psychosis risk. These results may have relevance for our understanding of the increased rates of paranoia and psychotic disorders in ethnic minority individuals.
ESPSearch: a program for finding exact sequences and patterns in DNA, RNA, or protein.

ESPSearch is a computer program for rapidly identifying nucleic acid or amino acid sequences of any length within any source sequence from promoters to entire genomes to protein libraries. ESPSearch utilizes a user-constructed database to identify many sequences simultaneously, including target sequences with wildcards and mismatches and user-specified patterns of those recognized sequences. Here we use ESPSearch to identify a variety of possible binding sites for dimeric artificial transcription factors within several p53 recognition sites and the promoter of the BAX gene. Heterodimeric and homodimeric proteins are designed using human zinc fingers by identifying groups of zinc finger binding sites meeting particular pattern constraints. ESPSearch is also used to estimate the specificity of each artificial transcription factor by searching the entire genome. Next, the specificity of several possible small interfering RNA (siRNA) sequences is determined by searching both the whole genome and the library of known human mRNAs. Finally, ESPSearch identifies proteins containing different forms of the LXXLL motif used in nuclear receptor-coactivator interactions from the human proteome, making use of user-defined groups of amino acids. ESPSearch could also be applied to other tasks involving sequence and pattern recognition on small and large scales. ESPSearch is freely available at http://web.chemistry. gatech.edu/-doyle/espsearch/.
Isolation, cDNA cloning, and overexpression of a 33-kD cell surface glycoprotein that binds to the globular "heads" of C1q

This work describes the functional characterization, cDNA cloning, and expression of a novel cell surface protein. This protein designated gC1q-R, was first isolated from Raji cells and was found to bind to the globular "heads" of C1q molecules, at physiological ionic strength, and also to inhibit complement-mediated lysis of sheep erythrocytes by human serum. The NH2-terminal amino acid sequence of the first 24 residues of the C1q-binding protein was determined and this information allowed the synthesis of two degenerate polymerase chain reaction primers for use in the preparation of a probe in the screening of a B cell cDNA library. The cDNA isolated, using this probe, was found to encode a pre-pro protein of 282 residues. The NH2 terminus of the protein isolated from Raji cells started at residue 74 of the predicted pre-pro sequence. The cDNA sequence shows that the purified protein has three potential N-glycosylation residues and is a highly charged, acidic molecule. Hence, its binding to C1q may be primarily but not exclusively due to ionic interactions. The "mature" protein, corresponding to amino acid residues 74-282 of the predicted pre-pro sequence, was overexpressed in Escherichia coli and was purified to homogeneity. This recombinant protein was also able to inhibit the complement-mediated lysis of sheep erythrocytes by human serum and was shown to be a tetramer by gel filtration in nondissociating conditions. Northern blot and RT-PCR studies showed that the C1q-binding protein is expressed at high levels in Raji and Daudi cell lines, at moderate levels in U937, Molt-4, and HepG2 cell lines, and at a very low level in the HL60 cell line. However, it is not expressed in the K562 cell line. Comparison of gC1q-R NH2-terminal sequence with that of the receptor for the collagen-like domain of C1q (cC1q-R) showed no similarity. Furthermore, antibodies to gC1q-R or an 18-amino acid residue-long NH2-terminal synthetic gC1q-R peptide did not cross-react with antibodies to cC1q-R. Anti-gC1q-R immunoblotted a 33-kD Raji cell membrane protein, whereas anti cC1q-R recognized a molecule of approximately 60 kD. The NH2-terminal sequence of gC1g-R appears to be displayed extracellularly since anti-gC1g-R peptide reacted with surface molecules on lymphocytes, polymorphonuclear leukocytes, and platelets, as assessed by flow cytometric and confocal laser scanning microscopic analyses. (ABSTRACT TRUNCATED AT 400 WORDS)
Colorization-Based RGB-White Color Interpolation using Color Filter Array with Randomly Sampled Pattern

Recently, several RGB-White (RGBW) color filter arrays (CFAs) have been proposed, which have extra white (W) pixels in the filter array that are highly sensitive. Due to the high sensitivity, the W pixels have better SNR (Signal to Noise Ratio) characteristics than other color pixels in the filter array, especially, in low light conditions. However, most of the RGBW CFAs are designed so that the acquired RGBW pattern image can be converted into the conventional Bayer pattern image, which is then again converted into the final color image by using conventional demosaicing methods, i.e., color interpolation techniques. In this paper, we propose a new RGBW color filter array based on a totally different color interpolation technique, the colorization algorithm. The colorization algorithm was initially proposed for colorizing a gray image into a color image using a small number of color seeds. Here, we adopt this algorithm as a color interpolation technique, so that the RGBW color filter array can be designed with a very large number of W pixels to make the most of the highly sensitive characteristics of the W channel. The resulting RGBW color filter array has a pattern with a large proportion of W pixels, while the small-numbered RGB pixels are randomly distributed over the array. The colorization algorithm makes it possible to reconstruct the colors from such a small number of RGB values. Due to the large proportion of W pixels, the reconstructed color image has a high SNR value, especially higher than those of conventional CFAs in low light condition. Experimental results show that many important information which are not perceived in color images reconstructed with conventional CFAs are perceived in the images reconstructed with the proposed method.
The Fractality of Polar and Reed–Muller Codes †

The generator matrices of polar codes and Reed–Muller codes are submatrices of the Kronecker product of a lower-triangular binary square matrix. For polar codes, the submatrix is generated by selecting rows according to their Bhattacharyya parameter, which is related to the error probability of sequential decoding. For Reed–Muller codes, the submatrix is generated by selecting rows according to their Hamming weight. In this work, we investigate the properties of the index sets selecting those rows, in the limit as the blocklength tends to infinity. We compute the Lebesgue measure and the Hausdorff dimension of these sets. We furthermore show that these sets are finely structured and self-similar in a well-defined sense, i.e., they have properties that are common to fractals.
Substernal Goiter: When is a Sternotomy Required?

The presence of substernal goiter is, per se, an indication for surgical management. Surgical approach of substernal goiter can most commonly be performed using the cervical access, but at times, a sternotomy or thoracotomy is necessary. The aim of this study was to identify the preoperative predictors of a sternotomy in the management of substernal goiter in order to provide better preoperative planning and patient consent. Between 2005 and 2012, 665 patients were referred to our clinic for thyroidectomy, 42 patients (6.3%) had substernal goiter and were included in this study. All substernal goiters were treated surgically, 38 (90.5%) by a cervical approach and 4 (9.5%) by full median sternotomy. All surgeries were successful, with no major postoperative complications. Minor postoperative complications of transient hypocalcemia and transient paralysis of the recurrent laryngeal nerve occurred in 5 (11.9%) and 2 (4.7%) cases, respectively. Indication of median sternotomy was as follows: extension of goiter below the aortic arch, large thyroid tissue extending towards tracheal bifurcation, and ectopic thyroid tissue in the mediastinum. Substernal goiter can be removed through a cervical incision, but on rare occasions, a median sternotomy may be required.
Changes in pain and quality of life in depressed individuals with spinal cord injury: does type of pain matter?

Objective: To examine the association of neuropathic and nociceptive pain severity and interference with quality of life (QoL) in persons with spinal cord injury (SCI) who underwent a randomized controlled 12-week trial of an antidepressant to treat depression. A secondary objective was to assess the effect of changes in pain on mobility and physical independence. Design: Multivariable ANCOVA models controlling for relevant demographic covariates, treatment condition, and baseline pain and QoL were used. Setting: Six rehabilitation centers. Participants: Of the 133 persons who were randomized into the trial, 108 provided pain severity and interference ratings through follow-up. Interventions: Not applicable. Outcome Measures: The Satisfaction with Life Scale and the physical and mental component summary scores of the 12-Item Short-Form Health Survey (SF-12). Secondary outcome measures included the mobility and physical independence subscales of the Craig Handicap Assessment and Reporting Technique (CHART). Results: Broadly, few associations between pain and QoL were evident. Results revealed relationships between lower baseline nociceptive pain interference and higher satisfaction with life and mental health-related QoL at 12 weeks. Similarly, lower neuropathic pain interference was associated with change in physical independence, but unrelated to mobility. Conclusions: Pain interference over time may be differentially related to QoL outcomes based on the type of pain following SCI, but overall, there were no extensive relationships between pain and QoL in this sample of depressed persons with SCI.
A Formal Approach to the Selection by Minimum Error and Pattern Method for Sensor Data Loss Reduction in Unstable Wireless Sensor Network Communications

There are wireless networks in which typically communications are unsafe. Most terrestrial wireless sensor networks belong to this category of networks. Another example of an unsafe communication network is an underwater acoustic sensor network (UWASN). In UWASNs in particular, communication failures occur frequently and the failure durations can range from seconds up to a few hours, days, or even weeks. These communication failures can cause data losses significant enough to seriously damage human life or property, depending on their application areas. In this paper, we propose a framework to reduce sensor data loss during communication failures and we present a formal approach to the Selection by Minimum Error and Pattern (SMEP) method that plays the most important role for the reduction in sensor data loss under the proposed framework. The SMEP method is compared with other methods to validate its effectiveness through experiments using real-field sensor data sets. Moreover, based on our experimental results and performance comparisons, the SMEP method has been validated to be better than others in terms of the average sensor data value error rate caused by sensor data loss.
On the Broadcast Routing Problem in Computer Networks

Given an undirected graph $G = (V, E)$, and a vertex $r\in V$, an $r$-acyclic orientation of $G$ is an orientation $OE$ of the edges of $G$ such that the digraph $OG = (V, OE)$ is acyclic and $r$ is the unique vertex with indegree equal to 0. For $w\in \mathbb{R}^E_+$, $k(G, w)$ is the value of the $w$-maximum packing of $r$-arborescences for all $r\in V$ and all $r$-acyclic orientations $OE$ of $G$. In this case, the Broadcast Routing (in Computers Networks) Problem (BRP) is to compute $k(G, w)$, by finding an optimal $r$ and an optimal $r$-acyclic orientation. BRP is a mathematical formulation of multipath broadcast routing in computer networks. In this paper, we provide a polynomial time algorithm to solve BRP in outerplanar graphs. Outerplanar graphs are encountered in many applications such as computational geometry, robotics, etc.
ONE-TO-ONE NONLINEAR TRANSFORMATION OF THE SPACE WITH IDENTITY PLANE

Purpose. Study of geometric transformations. We will consider the so-called point transformations of space. Methodology. The most important are one-to-one transformations. They allow exploring and studying the properties of the transformed object using the properties of the original object (line, surface and figure) and the properties of the transformation. Cremona transformations occupy a special place in the set of one-to-one nonlinear transformations. Construction of one-parameter (stratifiable) transformations is carried out as one-parameter set of plane transformations, both linear and non-linear ones. The plane, in which the specific transformation is prescribed, moves in space by a certain law forming a one-parameter set of planes. The set of such plane transformations makes up the space transformation. Findings. The designed graphics algorithms and the established transformation equations allow building the visual images of transformed surfaces and conducting their research by analytical geometry methods. Originality. By completing elementary algebraic transformations of this equation, we obtain the cissoids equation. If the plane is continuously moved parallel to itself, it results in occurrence of surface, whose carcass will be the set of cissoids and the set of front-projecting lines. Practical value. The considered set of stratifiable algebraic transformations gives an effective means for exploring new curves and surfaces obtained by transforming the known algebraic lines and surfaces. These graphic algorithms allow graphically depicting the transformed lines and surfaces. The considered procedure of drawing up analytical formulas of specific transformations allows us to study the transformed surfaces and lines using the methods of analytic geometry. The above transformations can be of arbitrary high order, which is especially important during the design of complex technical surfaces such as aircraft components, parts of water and gas turbines, supports of the structures subject to strong flow of liquid, etc. Space modelling issues, including the building of graphic plane models of space, are relevant both in theoretical terms and in terms of application of the non-linear surfaces investigated on their basis for constructing the technical forms of parts and aggregates of construction machine movable elements, the middle surfaces of shells, the surfaces of turbulent blade, etc.
Quadriceps Strength Deficit at 6 Months After ACL Reconstruction Does Not Predict Return to Preinjury Sports Level

Background: There is a lack of literature-based objective criteria for return to sport after anterior cruciate ligament (ACL) injury. Establishing such objective criteria is crucial to improving return to sport after ACL reconstruction (ACLR). Hypotheses: Patients who return to their preinjury level of sport will have higher isokinetic, postural stability, and drop vertical jump test scores 6 months after surgery and greater patient satisfaction compared with those who did not. Additionally, quadriceps strength deficit cutoff values of 80% and 90% would differentiate patients who returned to preinjury sports level from those who did not. Study Design: Cohort study. Level of Evidence: Level 3. Methods: A retrospective search was conducted to identify all patients who underwent ACLR and completed isokinetic evaluation, postural stability analysis, and drop vertical jump testing at 6 months postoperatively. Patients were asked to complete 3 questionnaires at a minimum 1 year after surgery. Chi-square and logistic regression analyses were used for categorical dependent variables, while the Student t test, Pearson correlation, or analyses of variance with Bonferroni post hoc testing were used for continuous dependent variables. A post hoc power analysis was completed. Based on the results regarding correlations between return to preinjury level and all other variables, effect sizes from 0.24 to 3.03 were calculated. With these effect sizes, an alpha of 0.05 and sample size of 58, a power ranging from 0.15 to 0.94 was calculated. Results: The rates of return to preinjury level and to any sports activity were 53.4% and 84.4%. Those who were able to return to their preinjury level of sport (n = 33) showed significantly higher Lysholm (91.6 ± 9.7 vs 76.7 ± 15.4) and International Knee Documentation Committee (IKDC) (83.6 ± 10.6 vs 69.8 ± 14.6) values compared with those who were unable to return to their preinjury level of sport (n = 25) (P < 0.001). No significant differences were found for the clinical evaluations between those who were and those who were not able to return at the same level for the clinical evaluations (isokinetic evaluation, postural stability, drop vertical jump test) (P > 0.05). No significant differences were found when comparing quadriceps strength deficit with cutoff values of 80% and 90% for return to preinjury activity level (Tegner), Lysholm, and IKDC scores. Conclusion: Quadriceps strength deficit, regardless of cutoff value (80% or 90%), at 6 months after ACLR does not predict return to preinjury level of sport. Patients who returned to sport at their preinjury level were more satisfied with their reconstruction compared with those who did not. Clinical Relevance: Quadriceps strength deficit is not a reliable predictor of return to sports, and therefore it should not be used as the single criterion in such evaluations.
Optimizing Odor-Baited Trap Methods for Collecting Mosquitoes during the Malaria Season in The Gambia

Background Baited traps are potential tools for removal or surveillance of disease vectors. To optimize the use of counter-flow traps baited with human odor (nylon socks that had been worn for a single day) to capture wild mosquitoes in the Gambia, investigations were conducted at a field experimental site. Methodology/Principal Findings Experiments employing Latin square design were conducted with a set of six huts to investigate the effects of the following on overnight mosquito trap catches: (1) placement of traps indoors or immediately outdoors, CO2 supply, and presence of a human subject in the hut; (2) trap height for collecting mosquitoes immediately outdoors; (3) height and distance from hut; (4) interaction between multiple traps around a single hut and entry of mosquitoes into huts. A total of 106,600 adult mosquitoes (9.1% Anopheles gambiae s.l., 4.0% other Anopheles species) were collected over 42 nights. The high numbers of An. gambiae s.l. and other mosquitoes collected by odor-baited traps required CO2 but were largely independent of the presence of a person sleeping in the hut or of trap placement indoors or outdoors. For outdoor collection that is considered less intrusive, traps opening 15 cm above the floor of the hut veranda were more highly effective than traps at other heights or further from the hut. There was no significant evidence of saturation or competition by the traps, with multiple traps around a hut each collecting almost as many mosquitoes as single traps and no effect on the numbers of mosquitoes entering the huts. Conclusions/Significance The outdoor trapping protocol is convenient to compare attractiveness of different odors or synthetic chemicals to malaria vectors and other wild mosquitoes. The finding that such traps are reliably attractive in the presence or absence of a human volunteer encourages their potential development as standardised surveillance tools.