Figure mining for biomedical research

Motivation: Figures from biomedical articles contain valuable information difficult to reach without specialized tools. Currently, there is no search engine that can retrieve specific figure types. Results: This study describes a retrieval method that takes advantage of principles in image understanding, text mining and optical character recognition (OCR) to retrieve figure types defined conceptually. A search engine was developed to retrieve tables and figure types to aid computational and experimental research. Availability: http://iossifovlab.cshl.edu/figurome Contact: [email protected]

Micosis Fungoide en un perro

Se describe un caso de Micosis Fungoide (MF) en un perro mestizo de 10 años de edad. El animal presentaba una dermatosis multifocal prurítica y simétrica que afectaba a la cabeza, abdomen, ingles, axilas y membranas mucosas., Las principales lesiones eran eritemas, placas, pápulas, pústulas y ulceraciones. Inicialmente se sospechó un pénfigo vulgaris pero los estudios histopatológícos y el test de inmunofluorescencia directa (negativo) evidenciaron que se trataba de una MF.We describe a case of Mycosis Fungoides (MF) in a 10 years old mixed-breed dog. The animal showed a pruritic multifocal dermatosis which affected bead, abdomen, axillae, groins and mucous membranes. Main lesions inciuded erytherna, plaques; papuies, pus tules and ulceration. First a pemphigus vulgaris was suspeaed but histopathology and direct immunofluorescence testing (negative) showed that it was a M.F

Functional correlates of response inhibition in impulse control disorders in Parkinson’s disease

Impulse control disorder is a prevalent side-effect of Parkinson’s disease (PD) medication, with a strong negative impact on the quality of life of those affected. Although impulsivity has classically been associated with response inhibition deficits, previous evidence from PD patients with impulse control disorder (ICD) has not revealed behavioral dysfunction in response inhibition. In this study, 18 PD patients with ICD, 17 PD patients without this complication, and 15 healthy controls performed a version of the conditional Stop Signal Task during functional magnetic resonance imaging. Whole-brain contrasts, regions of interest, and functional connectivity analyses were conducted. Our aim was to investigate the neural underpinnings of two aspects of response inhibition: proactive inhibition, inhibition that has been prepared beforehand, and restrained inhibition, inhibition of an invalid inhibitory tendency. We observed that, in respect to the other two groups, PD patients with ICD exhibited hyperactivation of the stopping network bilaterally while performing proactive inhibition. When engaged in restrained inhibition, they showed hyperactivation of the left inferior frontal gyrus, an area linked to action monitoring. Restrained inhibition also resulted in changes to the functional co-activation between inhibitory regions and left inferior parietal cortex and right supramarginal gyrus. Our findings indicate that PD patients with ICD completed the inhibition task correctly, showing altered engagement of inhibitory and attentional areas. During proactive inhibition they showed bilateral hyperactivation of two inhibitory regions, while during restrained inhibition they showed additional involvement of attentional areas responsible for alerting and orientin

Enteric fever: a slow response to an old plague

Man is irremediably embedded in nature with complex interactions with all living organisms. Historically, the establishment of contemporary human societies has been influenced by our coexistence with other microorganisms living in highly interconnected habitats and ecologies. As a result, with the progression from unicellular to multicellular life, bacteria have coexisted with humans. In this biological journey, while there are important benefits provided by bacterial guests to the human host living in complex relationships and becoming part of their microbiome, some organisms are able to cause a wide spectrum of diseases. Among the large Enterobacteriaceae family, the genus Salmonella, a pathotype of Escherichia coli, is one example. Salmonella is further classified into S. enterica and S. bongori serotypes based on its lipopolysaccharide cell wall (somatic O antigen), its flagellar (H antigen), and its surface Vi antigen (present only in S. typhi, S. Paratyphi C, Citrobacter freundii, and S. Dublin) [1]. S. enterica subspecies I, one of the six subspecies of S. enterica, is a major contributor to human disease (Fig 1) [2]. This group of pathogens includes those frequently causing gastroenteritis, such as S. Typhimurium, those causing invasive disease in the forms of bacteremia, such as S. Choleraesius, or the typhoidal Salmonella species causing enteric fever, including S. typhi (typhoid fever) and S. Paratyphi A, B, and C (paratyphoid fever) [1,2]

Slow oscillatory activity and levodopa-induced dyskinesias in Parkinson’s disease

The pathophysiology of levodopa-induced dyskinesias (LID) in Parkinson’s disease is not well understood. We have recorded local field potentials (LFP) from macroelectrodes implanted in the subthalamic nucleus (STN) of 14 patients with Parkinson’s disease following surgical treatment with deep brain stimulation. Patients were studied in the ‘Off’ medication state and in the ‘On’ motor state after administration of levodopa– carbidopa (po) or apomorphine (sc) that elicited dyskinesias in 11 patients. The logarithm of the power spectrum of the LFP in selected frequency bands (4–10, 11–30 and 60–80 Hz) was compared between the ‘Off’ and ‘On’ medication states. A peak in the 11–30 Hz band was recorded in the ‘Off’ medication state and reduced by 45.2% (P < 0.001) in the ‘On’ state. The ‘On’ was also associated with an increment of 77. 6% (P < 0.001) in the 4–10 Hz band in all patients who showed dyskinesias and of 17.8% (P < 0.001) in the 60–80 Hz band in the majority of patients. When dyskinesias were only present in one limb (n = 2), the 4–10 Hz peak was only recorded in the contralateralSTN. These findings suggest that the 4–10 Hz oscillation is associated with the expression of LID in Parkinson’s disease

Physical activity and amyloid beta in middle-aged and older adults:A systematic review and meta-analysis

Background: One of the pathological hallmarks distinguishing Alzheimer's disease from other dementias is the accumulation of amyloid beta (Aβ). Higher physical activity is associated with decreased dementia risk, and one potential path could be through Aβ levels modulation. We aimed to explore the relationship between physical activity and Aβ in middle-aged and older adults. Methods: A systematic search of PubMed, Web of Science, PsycINFO, Cochrane Central Register of Controlled Trials, and SPORTDiscus was performed from inception to the 28th of April 2022. Studies were eligible if they included physical activity and Aβ data in adults aged 45 years or older. Multi-level meta-analyses of intervention and observational studies were performed to examine the role of physical activity in modulating Aβ levels. Results: In total, 37 articles were included (8 randomized controlled trials, 3 non-randomized controlled trials, 4 prospective longitudinal studies, and 22 cross-sectional studies). The overall effect size of physical activity interventions on changes in blood Aβ was medium (pooled standardized mean difference = –0.69, 95% confidence interval (95%CI): –1.41 to 0.03; I2 = 74.6%). However, these results were not statistically significant, and there were not enough studies to explore the effects of physical activity on cerebrospinal fluid (CSF) and brain Aβ. Data from observational studies were examined based on measurements of Aβ in the brain using positron emission tomography scans, CSF, and blood. Higher physical activity was positively associated with Aβ only in the CSF (Estimate r = 0.12; 95%CI: 0.05–0.18; I2 = 38%). Conclusion: Physical activity might moderately reduce blood Aβ in middle-aged and older adults. However, results were only near statistical significance and might be interpreted with caution given the methodological limitations observed in some of the included studies. In observational studies, higher levels of physical activity were positively associated with Aβ only in CSF. Therefore, further research is needed to understand the modulating role of physical activity in the brain, CSF, and blood Aβ, as well as its implication for cognitive health.</p

Synergy of DNA intercalation and catalytic activity of a copper complex towards improved polymerase inhibition and cancer cell cytotoxicity

Improving the binding of metal complexes to DNA to boost cancer cell cytotoxicity requires fine tuning of their structural and chemical properties. Copper has been used as a metal center in compounds containing intercalating ligands due to its ability to catalytically generate reactive oxygen species (ROS), such as hydroxyl radicals (OH˙). We envision the synergy of DNA binding and ROS generation in proximity to target DNA as a powerful chemotherapy treatment. Here, we explore the use of [Cu(2CP-Bz-SMe)]2+(2CP-Bz-SMe = 1,3-bis(1,10-phenanthrolin-2-yloxy)-N-(4-(methylthio)benzylidene)propan-2-amine) for this purpose by characterizing its cytotoxicity, DNA binding, and ability to affect DNA replication through the polymerase chain reaction - PCR and nuclease assays. We determined the binding (Kb) and Stern-Volmer constants (KSV) for complex-DNA association of 5.8 ± 0.14 × 104and 1.64 (±0.08), respectively, through absorption titration and competitive fluorescence experiments. These values were superior to those of other Cu-complex intercalators. We hypothesize that the distorted trigonal bipyramidal geometry of [Cu(2CP-Bz-SMe)]2+allows the phenanthroline fragments to be better accommodated into the DNA double helix. Moreover, the aromaticity of these fragments increases the local hydrophobicity thus increasing the affinity for the hydrophobic domains of DNA. Nuclease assays in the presence of common reducing agents ascorbic acid, nicotinamide adenine dinucleotide, and glutathione showed the effective degradation of DNA due to thein situgeneration of OH˙. The [Cu(2CP-Bz-SMe)]2+complex showed cytotoxicity against the following human cancer cells lines A549, MCF-7, MDA-MB-231 and MG-63 with half maximal inhibitory concentration (IC50) values of 4.62 ± 0.48, 5.20 ± 0.76, 5.70 ± 0.42 and 2.88 ± 0.66 μM, respectively. These low values of IC50, which are promising if compared to that of cisplatin, are ascribed to the synergistic effect of ROS generation with the intercalation ability into the DNA minor grooves and blocking DNA replication. This study introduces new principles for synergizing the chemical and structural properties of intercalation compounds for improved drug-DNA interactions targeting cancer.Fil: Romo, Adolfo I. B.. University of Illinois. Urbana - Champaign; Estados Unidos. Universidade Federal do Ceara; BrasilFil: Carepo, Marta P.. Universidade Nova de Lisboa; PortugalFil: Levin, Pedro. Universidad de Santiago de Chile; ChileFil: Nascimento, Otaciro R.. Universidade Federal do São Carlos; BrasilFil: Díaz, Daniel E.. Universidad de Santiago de Chile; ChileFil: Rodriguez Lopez, Joaquin. University of Illinois. Urbana - Champaign; Estados UnidosFil: Leon, Ignacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Química Inorgánica "Dr. Pedro J. Aymonino". Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Química Inorgánica "Dr. Pedro J. Aymonino"; ArgentinaFil: Bezerra, Lucas F.. Universidade Federal do Ceara; BrasilFil: Lemus, Luis A.. Universidad de Santiago de Chile; ChileFil: Diógenes, Izaura C. N.. Universidade Federal do Ceara; Brasi

La gran erupción de hace 4.2 ka cal en Cerro Blanco, Zona Volcánica Central, Andes: nuevos datos sobre los depósitos eruptivos holocenos en la Puna sur y regiones adyacentes

The eruption of the Cerro Blanco Volcanic Complex, in the southern Puna, NW Argentina dated at 4410–4150 a cal BP, was investigated to produce new information on stratigraphy, geomorphology, physical volcanology, radiocarbon dating, petrography, and geochemistry. Identification of pre–, syn–, and post–caldera products allowed us to estimate the distribution of the Plinian fallout during the paroxysmal syn–caldera phase of the eruption. The new results provide evidence for a major rhyolitic explosive eruption that spread volcanic deposits over an area of ~500,000 km2, accumulating > 100 km3 of tephra (bulk volume). This last value exceeds the lower threshold of Volcanic Explosive Index (VEI) of 7. Ash-fall deposits mantled the region at distances > 400 km from source and thick pyroclastic-flow deposits filled neighbouring valleys up to 35 km away. This eruption is the largest documented during the past five millennia in the Central Volcanic Zone of the Andes, and is probably one of the largest Holocene explosive eruptions in the world. We have also identified two additional rhyolitic eruptions in the region from two other eruptive sources: one during the Early–Holocene and another in the Late–Holocene. The identification and characterisation of these significant volcanic events provide new constraints into regional Holocene geological and archaeological records, and offer extensive regional chronostratigraphic markers over a wide geographical area of South America.La erupción del Complejo Volcánico Cerro Blanco en el sur de la Puna, noroeste de Argentina (4410–4150 a BP) se investigó para obtener nueva información sobre estratigrafía, geomorfología, volcanología física, dataciones por radiocarbono, petrografía y geoquímica. La caracterización de los productos en relación a la evolución de la caldera de Cerro Blanco permitió estimar la distribución de los depósitos de ceniza de la fase paroxísmica Plineana de la erupción. Estos novedosos resultados evidencian una gran erupción explosiva riolítica que generó depósitos cineríticos en un área de aproximadamente 500.000 km2, acumulando > 100 km3 de tefra (volumen total). Este último valor supera el umbral inferior del Índice de Explosividad Volcánica (IEV) de 7. Los depósitos de caída de ceniza cubrieron la región, llegando a más de 400 km desde el Complejo Volcánico de Cerro Blanco, y los potentes depósitos de flujos piroclásticos rellenaron los valles vecinos alcanzando una distancia de 35 km. Esta erupción es la más grande documentada durante los últimos cinco milenios en la Zona Volcánica Central de los Andes y es probablemente una de las mayores erupciones explosivas holocenas del mundo. Además, se han identificado otras dos erupciones riolíticas en la región procedentes de otros dos centros eruptivos: una durante el Holoceno temprano y otra en el Holoceno tardío. La identificación y caracterización de estos grandes eventos volcánicos proporcionan nuevas guías para los registros geológicos y arqueológicos regionales del Holoceno, siendo marcadores cronostratigráficos de aplicación a una extensa área geográfica de América del Sur