Miracle-dz/UniFAR-FTUs huggingface dataset:
Graph coarse‐graining reveals differences in the module‐level structure of functional brain networks

Networks have become a standard tool for analyzing functional magnetic resonance imaging (fMRI) data. In this approach, brain areas and their functional connections are mapped to the nodes and links of a network. Even though this mapping reduces the complexity of the underlying data, it remains challenging to understand the structure of the resulting networks due to the large number of nodes and links. One solution is to partition networks into modules and then investigate the modules’ composition and relationship with brain functioning. While this approach works well for single networks, understanding differences between two networks by comparing their partitions is difficult and alternative approaches are thus necessary. To this end, we present a coarse‐graining framework that uses a single set of data‐driven modules as a frame of reference, enabling one to zoom out from the node‐ and link‐level details. As a result, differences in the module‐level connectivity can be understood in a transparent, statistically verifiable manner. We demonstrate the feasibility of the method by applying it to networks constructed from fMRI data recorded from 13 healthy subjects during rest and movie viewing. While independently partitioning the rest and movie networks is shown to yield little insight, the coarse‐graining framework enables one to pinpoint differences in the module‐level structure, such as the increased number of intra‐module links within the visual cortex during movie viewing. In addition to quantifying differences due to external stimuli, the approach could also be applied in clinical settings, such as comparing patients with healthy controls.
Lifetime Prevalences of Physical Diseases and Mental Disorders in Young Suicide Victims

Objective: Evaluation was done of a possible link between psychiatric and physical illnesses in suicide victims 25 years of age or younger. Methods: This was a follow-up study based on a 13-year database (n = 1,585) of all suicides committed during the years 1988 to 2000 in northern Finland with linkage to national hospital discharge registers. The setting for the study was the province of Oulu, located in northern Finland. Subjects comprised 202 male and 27 female suicide victims aged 25 years or less. Results: Despite the young age of the suicide victims, lifetime prevalence of physical illness was about 70% in both males and females. In relation to mental disorders, female suicide victims were affected significantly more (45%) than their male counterparts (21%). About 27% of the subjects with physical illnesses had also suffered from mental disorders, but the respective proportion among those without any physical illness was only 7%. An increased prevalence of mental disorders was found in victims with diseases of the skin and subcutaneous tissues, musculoskeletal, respiratory, and digestive systems. Furthermore, increased incidences of mental disorders were also noticed in connection with injuries, poisonings, and symptoms or signs of infectious diseases. Prevalence of mental disorders in these physical disease categories varied from 25% to 44%. Conclusion: We recommend a greater attention to young people with physical illnesses and other symptoms in the hope that such screening may lead to an early recognition of psychiatric disorders and suicidal tendencies. FHDR = Finnish Hospital Discharge Register; ICD = International Classification of Diseases.
Dopaminergic marker proteins in the substantia nigra of human immunodeficiency virus type 1-infected brains

With the advent of highly active antiretroviral therapy, human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) is becoming a more chronic, manageable disease; nevertheless, the prevalence of neurological complications of AIDS is increasing. In this study, protein levels of tyrosine hydroxylase (TH) and dopamine transporter (DAT) in the substantia nigra of HIV-infected brains and -seronegative controls were determined by immunoblotting. The immunoreactivity of neuronal specific enolase (NSE) was used to assess cell loss. Although there were no changes in levels of immunoreactive DAT or NSE proteins in HIV brains, levels of immunoreactive TH were significantly reduced, relative to controls. These results suggest that decreases in TH, the rate-limiting enzyme of dopamine synthesis, may be a factor in the neurological manifestations of HIV infection.
No further loss of dorsal root ganglion cells after axotomy in p75 neurotrophin receptor knockout mice

The role of the p75 neurotrophin receptor for neuronal survival after nerve crush was studied in L5 dorsal root ganglia (DRG) of knockout mice and controls with assumption‐free stereological methods. Numbers of neuronal A‐ and B‐cells were obtained using the optical fractionator and optical disector techniques. At birth, the total number of DRG neurons was 10,000 ± 2,600 in control mice compared with 5,100 ± 1,300 in p75 knockout mice. During postnatal development, 1,400 neuronal B‐cell bodies were lost in p75 knockouts (2P < 0.05) and 1,100 in controls (NS), whereas the A‐cell population remained stable. After a sciatic nerve crush, the total neuron loss in controls was 15.4% ± 3.5% (2P < 0.05) and 22.7% ± 5.1% (2P < 0.05) at days 14 and 42, respectively. In contrast, there was no loss in total number of neurons after crush in p75 knockout mice. Neuronal A‐cell number was unchanged after the crush in p75 knockouts as well as in controls at both times. At 14 days, the population of B‐cells was reduced by 24.8% ± 3.6% in controls and by 6.1% ± 3.5% in p75 knockouts, this difference being significant (2P < 0.001). At 42 days, the B‐cell loss was 29.6% ± 5.5% in controls and 4.2% ± 6.4% in p75 knockouts (2P < 0.001). In conclusion, the lack of the p75 receptor results in neuronal DRG cells that are resistant to nerve injury, pointing to a role for the receptor in apoptosis. J. Comp. Neurol. 459:242–250, 2003. © 2003 Wiley‐Liss, Inc.
Revealing Henle's fiber layer using spectral domain optical coherence tomography.

PURPOSE Spectral domain optical coherence tomography (SD-OCT) uses infrared light to visualize the reflectivity of structures of differing optical properties within the retina. Despite their presence on histologic studies, traditionally acquired SD-OCT images are unable to delineate the axons of photoreceptor nuclei, Henle's fiber layer (HFL). The authors present a new method to reliably identify HFL by varying the entry position of the SD-OCT beam through the pupil. METHODS Fifteen eyes from 11 subjects with normal vision were prospectively imaged using 1 of 2 commercial SD-OCT systems. For each eye, the entry position of the SD-OCT beam through the pupil was varied horizontally and vertically. The reflectivity of outer retinal layers was measured as a function of beam position, and thicknesses were recorded. RESULTS The reflectivity of HFL was directionally dependent and increased with eccentricity on the side of the fovea opposite the entry position. When HFL was included in the measurement, the thickness of the outer nuclear layer (ONL) of central horizontal B-scans increased by an average of 52% in three subjects quantified. Four cases of pathology, in which alterations to the normal macular geometry affected HFL intensity, were identified. CONCLUSIONS The authors demonstrated a novel method to distinguish HFL from true ONL. An accurate measurement of the ONL is critical to clinical studies measuring photoreceptor layer thickness using any SD-OCT system. Recognition of the optical properties of HFL can explain reflectivity changes imaged in this layer in association with macular pathology.
Metabolic engineering of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) composition in recombinant Salmonella enterica serovar typhimurium.

A recombinant strain of Salmonella enterica serovar Typhimurium (mutant in propionate-activation activity) was metabolically engineered to control the composition of poly(3-hydroxybutyrate-co-3-hydroxy- valerate) (PHBV), a polyhydroxyalkanoate copolymer with commercially desirable properties. A gene (prpE) encoding propionyl-CoA synthetase was placed under the control of the IPTG-inducible taclacUV5 promoter (P(taclacUV5)) while the polyhydroxyalkanoate synthesis operon (phaBCA) from Acinetobacter sp. RA3849 was coexpressed under the control of the arabinose-inducible araBAD promoter (P(BAD)). S. enterica, harboring both constructs, was grown in medium containing a fixed substrate concentration and the composition of the copolymer was varied between 2 mol% and 25 mol% 3-hydroxyvalerate by controlling the IPTG level in the medium. This "dial-a-composition" system should find application in cases where the substrate concentration of a feedstream for PHBV bioplastic production is not adjustable.
Solid-Phase Epitope Recovery: A High Throughput Method for Antigen Identification and Epitope Optimization

Self tolerance to MHC class I-restricted nonmutated self Ags is a significant hurdle to effective cancer immunotherapy. Compelling evidence is emerging that altered peptide ligands can be far more immunogenic than their corresponding native epitopes; however, there is no way to reliably predict which modifications will lead to enhanced native epitope-specific immune responses. We reasoned that this limitation could be overcome by devising an empirical screen in which the nearly complete combinatorial spectrum of peptides of optimal length can be rapidly assayed for reactivity with a MHC class I-restricted cytotoxic T cell clone. This method, solid-phase epitope recovery, quantitatively ranks all reactive peptides in the library and allows selection of altered peptide ligands having desirable immunogenic properties of interest. In contrast to rationally designed MHC anchor-modified peptides, peptides identified by the present method are highly substituted in predicted TCR contact residues and can reliably activate and expand effector cell populations in vitro which lyse target cells presenting the wild-type epitope. We demonstrate that solid-phase epitope recovery peptides corresponding to a poorly immunogenic epitope of the melanoma Ag, gp100, can reliably induce wild-type peptide-specific CTL using normal donor T cells in vitro. Furthermore, these peptides can complement one another to induce these responses in an overwhelming majority of normal individuals in vitro. These data provide a rationale for the design of superior vaccines comprising a mixture of structurally diverse yet functionally convergent peptides.
Automatic summarization of API reviews

With the proliferation of online developer forums as informal documentation, developers often share their opinions about the APIs they use. However, given the plethora of opinions available for an API in various online developer forums, it can be challenging for a developer to make informed decisions about the APIs. While automatic summarization of opinions have been explored for other domains (e.g., cameras, cars), we found little research that investigates the benefits of summaries of public API reviews. In this paper, we present two algorithms (statistical and aspect-based) to summarize opinions about APIs. To investigate the usefulness of the techniques, we developed, Opiner, an online opinion summarization engine that presents summaries of opinions using both our proposed techniques and existing six off-the-shelf techniques. We investigated the usefulness of Opiner using two case studies, both involving professional software engineers. We found that developers were interested to use our proposed summaries much more frequently than other summaries (daily vs once a year) and that while combined with Stack Overflow, Opiner helped developers to make the right decision with more accuracy and confidence and in less time.
Bile Salts: Natural Detergents for the Prevention of Sexually Transmitted Diseases

ABSTRACT The development of new, safe, topical microbicides for intravaginal use for the prevention of sexually transmitted diseases is imperative. Previous studies have suggested that bile salts may inhibit human immunodeficiency virus infection; however, their activities against other sexually transmitted pathogens have not been reported. To further explore the potential role of bile salts in preventing sexually transmitted diseases, we examined the in vitro activities and cytotoxicities of select bile salts against Chlamydia trachomatis, herpes simplex virus (types 1 and 2),Neisseria gonorrhoeae, and human immunodeficiency virus in comparison to those of nonoxynol-9 and benzalkonium chloride using both primary cells and cell lines derived from the human female genital tract. We found that taurolithocholic acid 3-sulfate and a combination of glycocholic acid and taurolithocholic acid 3-sulfate showed excellent activity against all of the pathogens assayed. Moreover, taurolithocholic acid 3-sulfate alone or in combination was less cytotoxic than nonoxynol-9 and benzalkonium chloride. Thus, taurolithocholic acid 3-sulfate alone or in combination warrants further evaluation as a candidate topical microbicidal agent.
Many Hands Make Light Work: The Role of Collaborative Management in Improving Environmental Information Management by Local Authorities

ABSTRACT What is the role of collaborative management (CM) in enhancing environmental outputs? Does CM enable local municipalities to be better environmental performers? The present article addresses these two questions by means of a study of all urban localities in Israel (80% response rate). The aims of the study are to contribute to current research in two main ways. First, by addressing the question: Does CM enable local municipalities to be better environmental performers? In doing so, the study expands the very small number of studies conducted to date that examine performance and policy outputs of collaboration versus collaboration processes and procedures. Second, the study contributes to enlarging the very small number of relatively large N studies on collaborative public management that examine policy outputs. The main finding of this study highlights the important and positive role of CM in regard to local authorities’ environmental outputs.
A method for determining baroreflex‐mediated sympathetic and parasympathetic control of the heart in pregnant and non‐pregnant sheep

1 The cardiac baroreflex was measured in four non‐pregnant and six pregnant ewes before and during β‐adrenoreceptor blockade with propranolol and before and during vagal blockade with atropine. Arterial pressure was raised by phenylephrine and lowered by sodium nitroprusside. The relationships between mean arterial pressure (MAP) and heart rate (HR), between MAP and heart rate variability (HRV) measured as the coefficient of variation (c.v.) of the mean pulse interval (PI), and between MAP and HRV measured by power spectral analysis were determined. 2 The MAP‐HR relationship showed that in pregnant ewes the gain of the cardiac baroreflex was reduced when compared with non‐pregnant ewes. Threshold and saturation pressures were higher, maximum achievable HR was lower and there was a decrease in the operating range. 3 V‐shaped relationships were obtained between MAP and HRV (measured as the c.v. of PI) and between MAP and power spectral density in the frequency range 0.04–0.08 Hz. Using selective autonomic blockade the negative, or downward, slope of the V shape was shown to be a measure of baroreceptor‐induced, sympathetically mediated effects on HRV. The upward, or positive, slope of the V shape was a measure of baroreceptor‐induced, vagally mediated effects. Similar results were also obtained from the cardiac power spectrum, but it was less sensitive. The MAP at which the two slopes intersected was the same as the resting MAP. 4 In pregnant ewes, the slope of the downward limb of the V‐shaped relationship between HRV (when measured as the c.v. of PI) and MAP was less than in non‐pregnant ewes. 5 The relationship between MAP and the coefficient of variation of the mean pulse interval can therefore be used to measure the degree to which baroreceptor‐induced sympathetic and parasympathetic activity affects the heart. 6 The resting MAP is the pressure at which the net effect of these sympathetic and parasympathetic influences on the heart is at a minimum. Studies of both the MAP‐HR and MAP‐HRV relationships in pregnant and non‐pregnant sheep show that in pregnant sheep, there is attenuation of baroreceptor‐mediated sympathetic effects on the heart.
Accuracy and reliability of cone beam computed tomographic measurements of the bone labial and palatal to the maxillary anterior teeth.

PURPOSE The aim of this study was to measure the thickness of bone labial and palatal to maxillary anterior teeth on cone beam computed tomographic (CBCT) images and to compare these measurements with direct clinical measurements to determine the reliability and accuracy of CBCT. MATERIALS AND METHODS Eighteen healthy subjects were randomly selected from among candidates for immediate implant placement in the anterior maxilla. After extraction, labial bone thickness was measured at 1, 4, and 8 mm from the bone crest. Palatal bone thickness was also measured at 1 and 4 mm from the bone crest. The same measurements were performed on presurgical CBCT images. The CBCT measurements were compared to the direct measurements, and their accuracy and reliability were assessed by Pearson correlation coefficients and intraclass correlation coefficients, respectively. RESULTS The mean width of labial bone was 0.50 ± 0.32 mm and 0.76 ± 0.37 mm for direct and CBCT measurements, respectively. Average thickness of the palatal bone was 1.16 ± 0.53 mm and 1.41 ± 0.51 mm for direct and CBCT measurements, respectively. The mean absolute error and mean relative error of CBCT measurements compared to direct measurements were 0.28 ± 0.29 mm and 0.60 ± 0.84 mm, respectively. The Pearson correlation between CBCT and direct measurements was 0.795 (P < .001) and the intraclass correlation coefficient between direct and CBCT measurements was 0.840. The correlation between the measurement series increased significantly when the measured bone was more than 1 mm thick. CONCLUSION CBCT measurements of labial bone mostly overestimated bone thickness. CBCT has relatively good accuracy and reliability for measurement of labial bone thickness when the alveolar bone is thicker than 1 mm. However, most subjects have labial bone thinner than 1 mm; therefore, CBCT could result in large errors in many patients.
Perception of Facial Profile: How You Feel About Yourself

Objective The aim of this study was to determine how aware the individuals were of their own profile and to compare the orthodontist’s perception of an attractive facial profile with those of laypeople, dental students and orthodontic patients. Materials and methods The study comprised of a total of 200 subjects divided into four groups of 50 subjects each: Laypeople, first-year dental students, final-year dental students and orthodontic patients. Participants answered a questionnaire regarding facial profile and their expectations from orthodontic treatment. The facial profile photographs of participants were analyzed by two orthodontists separately who matched the individual to the depicted silhouettes. Agreement between participants and orthodontists was evaluated by using the statistic χ2 test. Results Dental students and orthodontic patients were more aware of their facial profile as compared to the laypeople. The four groups were different in their abilities to recognize their own profiles. The difference in profile perception between orthodontists and subjects was statistically significant (p < 0.05). Conclusions Class I profiles were perceived to be the most attractive by all the groups and profiles with a protrusive mandible were perceived to be the least attractive. Final-year dental students and orthodontic patients were more accurate in identifying their own profile.
Chronic Recreational Physical Inactivity and Epithelial Ovarian Cancer Risk: Evidence from the Ovarian Cancer Association Consortium

Background: Despite a large body of literature evaluating the association between recreational physical activity and epithelial ovarian cancer (EOC) risk, the extant evidence is inconclusive, and little is known about the independent association between recreational physical inactivity and EOC risk. We conducted a pooled analysis of nine studies from the Ovarian Cancer Association Consortium to investigate the association between chronic recreational physical inactivity and EOC risk. Methods: In accordance with the 2008 Physical Activity Guidelines for Americans, women reporting no regular, weekly recreational physical activity were classified as inactive. Multivariable logistic regression was utilized to estimate the ORs and 95% confidence intervals (CI) for the association between inactivity and EOC risk overall and by subgroups based upon histotype, menopausal status, race, and body mass index. Results: The current analysis included data from 8,309 EOC patients and 12,612 controls. We observed a significant positive association between inactivity and EOC risk (OR = 1.34; 95% CI, 1.14–1.57), and similar associations were observed for each histotype. Conclusions: In this large pooled analysis examining the association between recreational physical inactivity and EOC risk, we observed consistent evidence of an association between chronic inactivity and all EOC histotypes. Impact: These data add to the growing body of evidence suggesting that inactivity is an independent risk factor for cancer. If the apparent association between inactivity and EOC risk is substantiated, additional work via targeted interventions should be pursued to characterize the dose of activity required to mitigate the risk of this highly fatal disease. Cancer Epidemiol Biomarkers Prev; 25(7); 1114–24. ©2016 AACR.
Effects of Antenatal Colonization with Ureaplasma urealyticum on Pulmonary Disease in the Immature Baboon

Current nonhuman models for bronchopulmonary dysplasia have not included perinatal infection. We studied the effects of antenatal Ureaplasma urealyticum (Uu) infection in the 125-d immature baboon. Ten 125-d gestation (term = 185 d) baboon dams were delivered after intra-amniotic inoculation with Uu. Serial blood and tracheal aspirate samples were analyzed for Uu colony-forming units, IL-6, IL-8, and cell counts. Physiologic parameters were serially recorded. Lung histology was examined after 14 d of ventilation and compared with unexposed controls. All Uu-exposed animals had >4 × 102 CFU in tracheal aspirate at 24 h. Four of nine Uu animals remained heavily colonized [(+) Uu] at necropsy (>6 × 103). Five animals had negative or low tracheal colony-forming units. All Uu animals had significant increases for white blood cells, IL-6, and IL-8 in amniotic and fetal lung fluid. Compared with controls, (+) Uu animals had significantly higher fraction of inspired oxygen, airway pressures, oxygenation index, and ventilation efficiency index between 48 and 240 h and had significantly elevated tracheal IL-6 and IL-8 concentrations between 72 and 240 h. Compared with controls (−) Uu animals had significantly better oxygenation index and ventilation efficiency index scores between 48 and 144 h. Lung histopathology in both Uu groups showed more severe bronchiolitis and interstitial pneumonitis compared with controls. Two patterns of disease were observed after Uu perinatal infection. Persistent colonization manifested a picture consistent with acute pneumonitis, worse lung function from 2 to 10 d, and prolonged elevated tracheal cytokines. Colonized animals that subsequently cleared Uu from the lung demonstrated early improved lung function compared with unexposed controls yet still manifested mixed bronchiolitis and interstitial pneumonitis at necropsy. Inherent immune system responses may determine outcome of perinatal Ureaplasma colonization.