Miracle-dz/UniFAR-FTUs huggingface dataset:
Review of advanced imaging techniques

Pathology informatics encompasses digital imaging and related applications. Several specialized microscopy techniques have emerged which permit the acquisition of digital images (“optical biopsies”) at high resolution. Coupled with fiber-optic and micro-optic components, some of these imaging techniques (e.g., optical coherence tomography) are now integrated with a wide range of imaging devices such as endoscopes, laparoscopes, catheters, and needles that enable imaging inside the body. These advanced imaging modalities have exciting diagnostic potential and introduce new opportunities in pathology. Therefore, it is important that pathology informaticists understand these advanced imaging techniques and the impact they have on pathology. This paper reviews several recently developed microscopic techniques, including diffraction-limited methods (e.g., confocal microscopy, 2-photon microscopy, 4Pi microscopy, and spatially modulated illumination microscopy) and subdiffraction techniques (e.g., photoactivated localization microscopy, stochastic optical reconstruction microscopy, and stimulated emission depletion microscopy). This article serves as a primer for pathology informaticists, highlighting the fundamentals and applications of advanced optical imaging techniques.
Leber's Hereditary Optic Neuropathy-Specific Mutation m.11778G>A Exists on Diverse Mitochondrial Haplogroups in India.

Purpose Leber's hereditary optic neuropathy (LHON; OMIM 535000) is one of the most common maternally inherited mitochondrial disorders. Three mitochondrial DNA point mutations-m.3460G>A (MT-ND1), m.11778G>A (MT-ND4), and m.14484T>C (MT-ND6)-account for the majority of reported LHON cases. Only approximately 50% of males and approximately 10% of females carrying these mutations develop optic neuropathy and blindness. Additional factors, such as mtDNA/nuclear genetic background and environmental modifiers, are likely to contribute toward the observed incomplete penetrance and gender bias. We aimed to investigate whether mtDNA haplogroup influences LHON clinical expression in Indian patients harboring the m.11778G>A mutation. Methods Detailed clinical assessment and complete mitochondrial genome sequencing was undertaken in 64 LHON families harboring the m.11778G>A mutation. Mitochondrial haplogroup was assigned based on evolutionarily conserved mtDNA variations. Results A total of 543 individuals (295 male, 248 female) from 64 unrelated families harboring the m.11778G>A mutation were recruited to the study. The overall disease penetrance was 27.07% (146 of 543) and higher in males (37.9%; 112 of 295) than females (13.7%; 34 of 248). The mtDNA haplogroup analysis revealed that all affected probands belonged to different mtDNA haplogroups. No association between the m.11778G>A mutation and the background mtDNA haplogroup was detected. Conclusions The first detailed study of Indian LHON patients confirm that the m.11778G>A-related LHON in India coexists with multiple different mtDNA haplogroups, unlike the preferential association of west Eurasian haplogroup J and the reported increased clinical penetrance with the J2 subhaplogroup. However, we observed variable penetrance of LHON in different Indian mtDNA haplogroup backgrounds, indicating their possible influence on clinical expression. These data suggest that a similar heterogeneity, resulting from the mtDNA haplogroup, might also exist in other mitochondrial diseases among Indian populations.
Targeting the interleukin-11 receptor α in metastatic prostate cancer: A first-in-man study

Receptors in tumor blood vessels are attractive targets for ligand‐directed drug discovery and development. The authors have worked systematically to map human endothelial receptors (“vascular zip codes”) within tumors through direct peptide library selection in cancer patients. Previously, they selected a ligand‐binding motif to the interleukin‐11 receptor alpha (IL‐11Rα) in the human vasculature.
Alternating Projections Methods for Discrete-Time Stabilization of Quantum States

We study sequences (both cyclic and randomized) of idempotent completely positive trace-preserving quantum maps, and show how they asymptotically converge to the intersection of their fixed point sets via alternating projection methods, highlighting the robustness features of the protocol against randomization. The general results are then specialized to stabilizing entangled states in finite-dimensional multipartite quantum systems subject to locality constraints, a problem of key interest for quantum information applications.
Vibration reduction for vision systems on board UAV using a neuro-fuzzy controller

In this paper, an intelligent control approach based on Neuro-Fuzzy systems performance is presented with the objective of counteracting the vibrations that affect the low-cost vision platform onboard an unmanned aerial system of rotating nature. A scaled dynamical model of a helicopter is used to simulate vibrations on its fuselage. The impact of these vibrations on the low-cost vision system will be assessed and an intelligent control approach will be derived in order to reduce its detrimental influence. Different trials that consider a Neuro-Fuzzy approach as a fundamental part of an intelligent semi-active control strategy have been carried out. Satisfactory results have been achieved compared to those obtained by means of vibration reduction passive techniques.
Conscientiousness Is Not Always a Good Predictor of Performance: The Case of Creativity

Meta-analyses investigating the relationship between Conscientiousness and performance suggest a positive relationship for a variety of criteria. However, recently it has been argued that Conscientiousness is not always a good predictor of performance, particularly for creative performance. Additionally, it has been suggested that Conscientiousness includes two distinct components, achievement and dependability, which may have different relationships with criterion measures. Two studies were conducted to determine whether the components of Conscientiousness predict creativity better than the full factor. Students in each study completed a measure of the Five Factor Model and a measure of creative performance. In the first study, creative accomplishments were measured and in the second study, creative problem solving was measured. As predicted, both studies revealed a cooperative suppression effect when analyzing the conscientiousness components together such that achievement was positively related and dependability negatively related to creative performance. Also, both studies showed that the overall Conscientiousness factor was not related to creativity.
Exploring Higher-Order Risk Effects

Higher-order risk effects play an important role in examining economic behavior under uncertainty. A precautionary demand for saving has been linked to the property of prudence and the property of temperance has been used to show how the presence of an unavoidable risk affects one’s behavior towards a second risk. These two properties also play key roles in aversion to negative skewness and to kurtosis, respectively. Both properties recently have been characterized by preferences over lottery pairs in simple 50-50 gambles. The simplicity of this characterization is ideal for experimental investigation. This paper reports the results of such experiments and concludes that there is behavioral evidence for prudence, but not for temperance. Implications of these results for both expected-utility and non-expected-utility models are examined.
Artificial light at night causes an unexpected increase in oxalate in developing male songbirds

We quantified the effect of artificial light at night on oxalate, a potential marker of sleep debt, in free-living developing songbirds. Rather than a decrease, as was found in sleep-deprived mammals, oxalate increased in male nestlings. This research indicates a sex-specific physiological impact of ALAN that warrants further investigation.
On the role of discriminative intelligibility model for speech intelligibility enhancement

This paper uses listening tests to directly evaluate two speech pre-enhancement algorithms that were published in earlier work. The models were previously evaluated using purely objective measures. The methods under study aim to increase speech intelligibility by applying an adaptive spectral shaping ﬁlter to the speech signal. In both algorithms the shape of the ﬁlter is adapted so as to maximise the intelligibility predicted by an objective intelligibility model. The ﬁrst algorithm uses ‘glimpse propor-tion’ as the measure of intelligibility (i.e. assuming intelligibility is proportional to the extent of energetic masking). In contrast, the second optimises the score of a statistical ‘microscopic’ intelligibility model that measures the degree of discrimination between the correct interpretation and competing incorrect interpretations of the utterance. Results show that a signiﬁcant intelligibility gain is obtained when the simple energetic masking model is employed, whereas the discriminative model currently fails to provide any intelligibility improvement.
Group sequential designs with prospectively planned rules for subpopulation enrichment

We propose a class of randomized trial designs aimed at gaining the advantages of wider generalizability and faster recruitment while mitigating the risks of including a population for which there is greater a priori uncertainty. We focus on testing null hypotheses for the overall population and a predefined subpopulation. Our designs have preplanned rules for modifying enrollment criteria based on data accrued at interim analyses. For example, enrollment can be restricted if the participants from a predefined subpopulation are not benefiting from the new treatment. Our designs have the following features: the multiple testing procedure fully leverages the correlation among statistics for different populations; the asymptotic familywise Type I error rate is strongly controlled; for outcomes that are binary or normally distributed, the decision rule and multiple testing procedure are functions of the data only through minimal sufficient statistics. Our designs incorporate standard group sequential boundaries for each population of interest; this may be helpful in communicating the designs, because many clinical investigators are familiar with such boundaries, which can be summarized succinctly in a single table or graph. We demonstrate these designs through simulations of a Phase III trial of a new treatment for stroke. User‐friendly, free software implementing these designs is described. Copyright © 2016 John Wiley & Sons, Ltd.
Assessment of crystallite size and strain of CaCu 3 Ti 4 O 12 prepared via conventional solid-state reaction

Assessment of crystallite size and strain of CaCu3Ti4O12 (CCTO) with multimodal crystallite size is relatively a challenging task. Various estimation methods (Debye–Scherrer, Williamson–Hall, Rietveld refinement and Variance) are usually gave variation results due to different parameter selections of peaks broadening, for example, average line and integral breath (average and total). The high accuracy of estimation method is essential in order to obtain the best estimated result as close as possible to the observed crystallite size. Therefore, this Letter presents the comparison of estimation methods in determining the crystalline size and strain of CCTO from XRD peak broadening. The result shows that each method gave a different crystallite size as far as various solutions are concern and also depicts that the strain is same. However, Rietveld refinement, Debye–Scherrer and variance methods showed a highly correlated with domain size as observed from transmission electron microscopy analysis, due to an exclusion of the instrumental errors.
Associations between coronary and carotid artery atherosclerosis in patients with inflammatory joint diseases

Objective Low association between cardiac symptoms and coronary artery disease (CAD) in patients with inflammatory joint diseases (IJD) demands for objective markers to improve cardiovascular risk stratification. Our main aim was to evaluate the prevalence and characteristics of CAD in patients with IJD with carotid artery plaques. Furthermore, we aimed to assess associations of carotid ultrasonographic findings and coronary plaques. Methods Eighty-six patients (61% female) with IJD (55 with rheumatoid arthritis, 21 with ankylosing spondylitis and 10 with psoriatic arthritis) and carotid artery plaque were referred to coronary CT angiography (CCTA). CAD was evaluated using the modified 17-segment American Heart Association model. Calcium score, plaque composition, segment involvement score and segment stenosis score were assessed and correlated to the carotid artery plaques and cardiovascular disease risk factors in logistic and linear regression analyses. Risk prediction models were tested with various cut-off values for associating variables. Results Fifty-five patients (66%) had CAD assessed by CCTA and 36 (43%) of these had coronary plaques defined as either mixed or soft. Eleven patients (13%) had obstructive CAD. The best risk prediction model (area under the curve: 0.832, 95% CI 0.730 to 0.935) included the combination of variables with cut-off values: age ≥55 years (OR: 12.18, 95% CI 2.80 to 53.05), the carotid-intima media thickness ≥0.7 mm (OR: 4.08, 95% CI 1.20 to 13.89) and carotid plaque height ≥1.5 mm (OR: 8.96, 95% CI 1.68 to 47.91), p<0.05. Conclusion Presence of carotid plaque is alone not sufficient to identify patients at risk for CAD, and a combination of ultrasonographic measurements may be useful in risk stratification of patients with IJD. Trial registration number NCT01389388, Results.
Community-wide distribution of predator–prey interaction strength in kelp forests

The strength of interactions between predators and their prey (interaction strength) varies enormously among species within ecological communities. Understanding the community-wide distribution of interaction strengths is vital, given that communities dominated by weak interactions may be more stable and resistant to invasion. In the oceans, previous studies have reported log-normal distributions of per capita interaction strength. We estimated the distribution of predator–prey interaction strengths within a subtidal speciose herbivore community (45 species). Laboratory experiments were used to determine maximum per capita interaction strengths for eight species of herbivores (including amphipods, isopods, gastropods, and sea urchins) that graze on giant kelp (Macrocystis pyrifera) microscopic stages. We found that maximum per capita interaction strength saturated as a function of individual herbivore biomass, likely caused by predator/prey size thresholds. Incorporating this nonlinearity, we predicted maximum per capita interaction strength for the remaining herbivore species. The resulting distribution of per capita interaction strengths was bimodal, in striking contrast to previous reports from other communities. Although small herbivores often had per capita interaction strengths similar to larger herbivores, their tendency to have greater densities in the field increased their potential impact as grazers. These results indicate that previous conclusions about the distributions of interaction strength in natural communities are not general, and that intermediate-sized predators can under realistic circumstances represent the most effective consumers in natural communities.
Biomechanics of the human uterus

The appropriate biomechanical function of the uterus is required for the execution of human reproduction. These functions range from aiding the transport of the embryo to the implantation site, to remodeling its tissue walls to host the placenta, to protecting the fetus during gestation, to contracting forcefully for a safe parturition and postpartum, to remodeling back to its nonpregnant condition to renew the cycle of menstruation. To serve these remarkably diverse functions, the uterus is optimally geared with evolving and contractile muscle and tissue layers that are cued by chemical, hormonal, electrical, and mechanical signals. The relationship between these highly active biological signaling mechanisms and uterine biomechanical function is not completely understood for normal reproductive processes and pathological conditions such as adenomyosis, endometriosis, infertility and preterm labor. Animal studies have illuminated the rich structural function of the uterus, particularly in pregnancy. In humans, medical imaging techniques in ultrasound and magnetic resonance have been combined with computational engineering techniques to characterize the uterus in vivo, and advanced experimental techniques have explored uterine function using ex vivo tissue samples. The collective evidence presented in this review gives an overall perspective on uterine biomechanics related to both its nonpregnant and pregnant function, highlighting open research topics in the field. Additionally, uterine disease and infertility are discussed in the context of tissue injury and repair processes and the role of computational modeling in uncovering etiologies of disease. WIREs Syst Biol Med 2017, 9:e1388. doi: 10.1002/wsbm.1388
Relational Contracting, Negotiation, and External Enforcement

We study relational contracting and renegotiation in environments with external enforcement of long-term contractual arrangements. A long-term contract governs the stage games that the contracting parties will play in the future (depending on verifiable stage-game outcomes) until they renegotiate. In a contractual equilibrium, the parties choose their individual actions rationally, jointly optimize when selecting a contract, and exercise their relative bargaining power. Our main result is that in a wide variety of settings, the optimal contract is semi-stationary, with stationary terms for all future periods but special terms for the current period. In each period the parties renegotiate to this same contract. For example, in a simple principal-agent model with a choice of costly monitoring technology, the optimal contract specifies mild monitoring for the current period but intense monitoring for future periods. Because the parties renegotiate in each new period, intense monitoring arises only off the equilibrium path after a failed renegotiation. (JEL C73, C78, D23, D86)
Suicide classification — clues and their use A study of 122 cases of suicide and undetermined manner of death

In order to identify clues to forensic pathologist’s classification of suicide, the forensic files of 100 consecutive cases of suicide, and 22 cases of undetermined manner of death, were analysed. Some specific causes of death, suicidal communication and other circumstantial evidence suggesting suicidal intent explained all but three classifications. Problematic cases concerned death by poisoning and by submersion, alcohol-dependent persons and subjects with positive blood alcohol concentration at autopsy. Guidelines to support the police investigation as well as the medico-legal examination can probably reduce the number of undetermined cases in cases of possible suicide. # 2002 Elsevier Science Ireland Ltd. All rights reserved.
Intermittent hypoxia in obstructive sleep apnoea mediates insulin resistance through adipose tissue inflammation

Obstructive sleep apnoea (OSA) is increasingly associated with insulin resistance. The underlying pathophysiology remains unclear but intermittent hypoxia (IH)-mediated inflammation and subsequent dysfunction of the adipose tissue has been hypothesised to play a key role. We tested this hypothesis employing a comprehensive translational approach using a murine IH model of lean and diet-induced obese mice, an innovative IH system for cell cultures and a tightly controlled patient cohort. IH led to the development of insulin resistance in mice, corrected for the degree of obesity, and reduced insulin-mediated glucose uptake in 3T3-L1 adipocytes, associated with inhibition of the insulin-signalling pathway and downregulation of insulin-receptor substrate-1 mRNA. Providing mechanistic insight, IH induced a pro-inflammatory phenotype of visceral adipose tissue in mice with pro-inflammatory M1 macrophage polarisation correlating with the severity of insulin resistance. Complimentary in vitro analysis demonstrated that IH led to M1 polarisation of THP1-derived macrophages. In subjects without comorbidities (n=186), OSA was independently associated with insulin resistance. Furthermore, we found an independent correlation of OSA severity with the M1 macrophage inflammatory marker sCD163. This study provides evidence that IH induces a pro-inflammatory phenotype of the adipose tissue, which may be a crucial link between OSA and the development of insulin resistance. Intermittent hypoxia induces inflammatory phenotype of adipose tissue leading to insulin resistance in sleep apnoea http://ow.ly/k1TX3091YBM
Prevalence of blaZ Gene and Performance of Phenotypic Tests to Detect Penicillinase in Staphylococcus aureus Isolates from Japan

Guidelines recommend that clinical laboratories perform phenotypic tests (nitrocefin-based test and penicillin 10-U [P10] or 1-U [P1] zone edge tests) to detect penicillinase in Staphylococcus aureus isolates. This study aimed to assess the prevalence of blaZ encoding penicillinase and perform various phenotypic tests in S. aureus isolates from Japan. We prospectively collected 200 methicillin-susceptible S. aureus isolates from June 2015 to January 2016 and performed six phenotypic tests (nitrocefin-based test, P10 zone edge test/P10 diffusion test, penicillin 2-U [P2] zone edge test/P2 diffusion test, and cloverleaf test) on each sample. We confirmed the presence of blaZ (two blaZ-positive isolates) using PCR. Using blaZ PCR as a standard, we observed a low sensitivity (50%) and positive predictive value (PPV, 50%) of the nitrocefin-based test, low PPV (18.2%) of the P10 zone edge test, low sensitivity (50%) of the P10 diffusion test, low PPV (50% and 22.2%) of the P2 zone edge test and P2 diffusion test, respectively, and low sensitivity (50%) of the cloverleaf test. These data suggest a low performance (sensitivity and PPV) of these six phenotypic tests because of the low prevalence (1%) of blaZ in S. aureus isolates from Japan.
Estimation of Hepatitis B Virus, Hepatitis C Virus, and Different Clinical Parameters in the Thalassemic Population of Capital Twin Cities of Pakistan

Hepatitis B and C are serious public health problems worldwide. Thalassemia patients are dependent on blood transfusions throughout their life and are at high risk of viral infections. The aim of this study was to estimate the prevalence of hepatitis B/C infections and different clinical parameters in multitransfused thalassemia population. In this study, 262 multitransfused β-thalassemia patients were enrolled from the capital twin cities of Pakistan. The presence of hepatitis B virus (HBV)/hepatitis C virus (HCV), alanine aminotransferase (ALT) level, serum creatinine, serum ferritin, hepatomegaly, splenomegaly, and splenectomy were analyzed. The overall prevalence of HBV and HCV was 3.08% and 55.73%, respectively, with 100% of patients older than 20 years had HCV infection. The ALT levels among HBV- and HCV-positive thalassemia patients were 92.62 ± 41.57 U/L and 98 ± 63.65 U/L, respectively; creatinine values observed were 0.4 ± 0.35 mg/dL (for HBV) and 0.39 ± 0.24 mg/dL (for HCV), while serum ferritin levels were 6865.87 ± 1649.13 ng/dL (for HBV) and 5445.95 ± 3059.28 ng/dL (for HCV). A total of 74.8% and 82.20% of HBV- and HCV-positive patients had hepatomegaly with an average increase in liver size of 4.17 and 4.33 cm, respectively. Splenomegaly was observed in 64.9% and 67.12% of HBV- and HCV-positive patients with an average increase in spleen size of 4 and 4.46 cm, respectively. Splenectomy was observed among 14.50% and 15.75% of HBV- and HCV-infected thalassemia patients. There is a strong need to properly screen blood before transfusions to reduce the future load of viral hepatitis from Pakistan.