[Comparison of two types of classification in functional dyspepsia; postprandial distress or epigastric pain vs a multidimensional cluster analysis using unsupervised learning]. / Comparación de dos tipos de clasificación en dispepsia funcional; distrés postprandial o dolor epig ástrico vs un an álisis multidimensional por conglomerados utilizando aprendizaje no supervisado.

Artificial intelligence methods using unsupervised learning tools can support problem solving by establishing unidentified grouping or classification patterns that allow typing subgroups for more individualized management. There are few studies that allow us to know the influence of digestive and extra-digestive symptoms in the classification of functional dyspepsia. This research carried out a cluster unsupervised learning analysis based on these symptoms to discriminate subtypes of dyspepsia and compare with one of the currently most accepted classifications. An exploratory cluster analysis was carried out in adults with functional dyspepsia according to digestive, extra-digestive and emotional symptoms. Grouping patterns were formed in such a way that within each group there was homogeneity in terms of the values adopted by each variable. The cluster analysis method was two-stage and the results of the classification pattern were compared with one of the most accepted classifications of functional dyspepsia. Of 184 cases, 157 met the inclusion criteria. The cluster analysis excluded 34 unclassifiable cases. Patients with type 1 dyspepsia (cluster one) presented improvement after treatment in 100% of cases, only a minority presented depressive symptoms. Patients with type 2 dyspepsia (cluster two) presented a higher probability of failure to treatment with proton pump inhibitor, suffered more frequently from sleep disorders, anxiety, depression, fibromyalgia, physical limitations or chronic pain of a non-digestive nature. This classification of dyspepsia by cluster analysis establishes a more holistic vision of dyspepsia in which extradigestive characteristics, affective symptoms, presence or absence of sleep disorders and chronic pain allow discriminating behavior and response to first-line management.

Inclusión body myositis: A differential diagnosis to consider in patients with myopathy refractory to immunosuppressants. Two case reports / Miopatía por cuerpos de inclusión: un diagnóstico diferencial que considerar en pacientes con miopatía refractaria a inmunosupresores. Reporte de 2 casos

ABSTRACT Inclusion body myositis is part of the group of inflammatory myopathies, representing 30% of this group of diseases, and is considered an orphan disease because its estimated prevalence is less than 5 per 10,000 inhabitants. It produces weakness and atrophy of the proximal and distal muscles. The pathophysiological mechanisms are mainly autoimmune, inflammatory, and degenerative. The cases are presented of two female patients who came to : the emergency department due to progressive loss of upper and lower limb strength, and progressive asymmetric muscle weakness.

RESUMEN La miositis por cuerpos de inclusión forma parte del grupo de las miopatías inflamatorias, de las que representa el 30%; es considerada una enfermedad huérfana, ya que se estima que su prevalencia es menor a 5 por cada 10.000 habitantes. Produce debilidad y atrofia de los músculos proximales y distales. Los mecanismos fisiopatológicos son principalmente autoinmunes, inflamatorios y degenerativos. Se presentan 2 casos de mujeres, quienes acudieron a urgencias por pérdida progresiva de la fuerza en miembros superiores e inferiores, con debilidad muscular asimétrica de curso progresivo.

Dexamethasone vs methylprednisolone high dose for Covid-19 pneumonia.

BACKGROUND: There is no effective therapy for the severe acute respiratory syndrome by coronavirus 2 (SARS-CoV2) responsible for the Coronavirus disease 2019 (Covid-19). To date, dexamethasone has shown a decrease in mortality in patients who require oxygen, especially those with invasive mechanical ventilation. However, it is unknown if another corticosteroid can be used, the optimal dose and its duration, to achieve a better clinical outcome. The objective of the study was to compare the differences in clinical outcome and laboratory results in hospitalized patients with severe SARS-CoV2 Pneumonia treated with dexamethasone at 6 mg doses versus patients treated with high-dose methylprednisolone. MATERIALS AND METHODS: Ambispective cohort study with survival analysis of 216 patients diagnosed with severe Covid-19 pneumonia confirmed by polymerase chain reaction for SARS-CoV2 by Berlin protocol, who were hospitalized in a high-complexity clinic in Medellín, Colombia. The patients should also have supplementary oxygen and radiological confirmation of Pneumonia by chest tomography. Sample size was not calculated since the total population that met the inclusion criteria was evaluated. 111 patients were treated with the institutional protocol with intravenous dexamethasone 6 mg QD for seven to 10 days if they required oxygen. Since September 15, 2020, the hospitalization protocol of the clinic was modified by the Infectious Diseases and Pulmonology service, recommending a high dose of methylprednisolone of 250 to 500 mg every day for three days with a subsequent change to oral prednisone 50 mg every day for 14 days. The protocol was not applied in the intensive care unit, where dexamethasone continued to be administered. The clinical outcome and differences in laboratory results of the patients who received dexamethasone vs. the prospective cohort that received methylprednisolone from September 15 to October 31, 2020, were evaluated. Follow-up was carried out by outpatient consultation one month after discharge or by telephone, inquiring about readmission or living-dead status. RESULTS: 216 patients had Covid-19 pneumonia documented by ground-glass imaging and alveolar pressure / inspired oxygen fraction (PaFi) less than 300. 111 patients received dexamethasone (DXM) and 105 received methylprednisolone (MTP). Patients in the DXM group evolved to severe ARDS in a higher proportion (26.1% vs 17.1% than the MTP group). Upon completion 4 days of treatment with parenteral corticosteroid, laboratory markers of severity decreased significantly in the group that received MTP, CRP 2.85 (2.3-3.8) vs 7.2 (5.4-9.8), (p-value < 0.0001), D-dimer 691 (612-847) vs 1083 (740-1565) (p-value = 0.04) and DHL 273 (244-289) vs 355 (270.6-422) (p-value = 0.01). After starting the corticosteroid, transfer to the intensive care unit (4.8% vs. 14.4%) and mortality (9,5% vs. 17.1%) was lower in the group that received MTP. Recovery time was shorter in patients treated with MTP, three days (3-4) vs. DXM 6 days (5-8) (p-value < 0.0001). At 30-day follow-up, 88 (92.6%) were alive in MTP vs 58 (63.1%) of those who received dexamethasone. CONCLUSIONS: In this study, the treatment of severe Covid-19 Pneumonia with high-dose methylprednisolone for three days followed by oral prednisone for 14 days, compared with 6 mg dexamethasone for 7 to 10 days, statistically significantly decreased the recovery time, the need for transfer to intensive care and the severity markers C-reactive protein (CRP), D-dimer and LDH. Randomized controlled studies with methylprednisolone are required to corroborate its effect, and studies in a population hospitalized in intensive care wards.

Vulneración a la integridad física de personas mayores: prevalencia del maltrato y factores asociados / Violation of the Physical Integrity of the Elderly: Prevalence of Abuse and Related Factors

Resumen El envejecimiento poblacional que experimenta actualmente América Latina trae consigo retos para la sociedad, como la prevención de la vulneración a los derechos humanos y libertades de las personas mayores y la eliminación de todas las formas de maltrato. La prevalencia de maltrato físico a personas mayores fue de 4,1%. Se presentó principalmente en mujeres, personas sin pareja y con ingreso económico. Además, fue más prevalente en personas mayores con riesgo de depresión, ante cedentes de pensamientos suicidas, insatisfacción con la salud y que convivían con familias disfuncionales. Los hallazgos de esta investigación muestran como las re laciones familiares pueden ser un factor clave a la hora de abordar la problemática del maltrato; además, las graves repercusiones que generan estos hechos sobre la víctima, como afectaciones no solo a la salud física sino también mental.

Abstract The ageing population currently experienced by Latin America brings with it cha llenges for society, such as the prevention of human rights violation and freedoms of the elderly, and the elimination of all forms of abuse. The prevalence of physical abuse for the elderly was 4.1%. It was mainly presented in women, people without a partner, and with financial income. In addition, it was more prevalent in older people at risk of depression, a history of suicidal thoughts, dissatisfaction with health, and living with dysfunctional families. The findings of this research show how family re lationships can be a key factor in addressing the problem of abuse. In addition, the serious impact of these facts on the victim, such as affectations not only to physical health, but also to mental health.

Ergotism, a relatively unknown mimic of vasculitis: A case report and review of literature / Ergotismo: un imitador poco conocido de vasculitis. Reporte de caso y revisión de la literatura

ABSTRACT Introduction: Ergotism is a vasospasm that affects visceral and peripheral muscle arteries. Classically, symmetrical involvement of lower limb arteries is described, and is often associated with a history of chronic consumption of ergotamine derived medications (Cafergot). Case report: A 22 year-old healthy man with infectious mononucleosis syndrome, who presented with a sudden onset of paraesthesias in the lower limbs, as well as livedo reticularis. The initial diagnosis was a medium-sized vessel vasculitis (polyarteritis nodosa). The symptoms were preceded by the administration of Cafergot for headache treatment, and resolved spontaneously. The magnetic resonance angiography (MRA) of the lower limbs showed occlusion of peroneal arteries, with filiform distal flow. Other infectious, autoimmune and cardiovascular origins were ruled out. Discussion: Ergotism is an important differential diagnosis in the study of the patient with vasculitis, especially in acute onset presentations. Its treatment is the suspension of the causal drug, with vasodilator and surgical vascular procedures, if necessary. Conclusions: Ergotism is an imitator of vasculitis, especially in young patients with a history of difficult to control migraine. The concomitant administration of CYP3A4 inhibitors (mainly, protease inhibitors and macrolides) enhances the toxic effects of ergot.

RESUMEN Introducción: El ergotismo es un vasoespasmo que afecta las arterias musculares periféricas y viscerales. Clásicamente se describe la afectación simétrica de las arterias de las extremidades inferiores, a menudo asociada con el consumo crónico de medicamentos derivados de ergotamina (Cafergot®). Caso clínico: Varón sano de 22 anos con síndrome de mononucleosis, presentó parestesias en las extremidades inferiores y livedo reticularis de forma súbita, el diagnóstico inicial fue una vasculitis de mediano vaso (poliarteritis nodosa). Los síntomas fueron precedidos por la administración de Cafergot® para el tratamiento de cefalea, y se resolvieron espontáneamente. La angiografía por resonancia magnética (ARM) de las extremidades inferiores mostró oclusión de las arterias peroneas, con flujo distal filiforme. Se descartaron otras etiologías infecciosas, autoinmunes y cardiovasculares. Discusión: Los ergotismos son un diagnóstico diferencial importante en el estudio del paciente con vasculitis, especialmente en presentaciones de inicio agudo. Su tratamiento es la suspensión del fármaco causal, vasodilatadores y procedimientos vasculares quirúrgicos, si es necesario. Conclusiones: El ergotismo es un imitador de vasculitis, especialmente en pacientes jóvenes con antecedentes de migrana de difícil control. La administración concomitante de inhibidores del CYP3A4 (principalmente, inhibidores de proteasa y macrólidos) potencia los efectos tóxicos del ergot.

[The perspective of migrants on access to health care in the context of austerity policies in Andalusia (Spain)]. / La perspectiva de personas migrantes sobre el acceso a la atención sanitaria en el contexto de políticas de austeridad en Andalucía.

OBJECTIVE: To conduct an assessment of migrant people regarding their access to the health system following entry into force of Royal Decree-Law 16/2012 along with the impact of economic cuts on such access. METHOD: Qualitative phenomenological study with semi-structured interviews, conducted in Andalusia (Spain), in two phases (2009-2010 and 2012-2013), with 36 participants. The sample was segmented by length of stay, nationality and area of residence. The nationalities of origin are Bolivia, Morocco and Romania. RESULTS: Elements facilitating access in both periods: regular administrative situation, possession of Individual Health Card, knowledge of the language, social networks and information. The results show differences in access to health care for migrants before and after the enforcement of the RDL 16/2012, within austerity policies. In the second period, access barriers such as waiting times or incompatibility of schedules are aggravated and the socio-economic and administrative conditions of participants worsen. CONCLUSIONS: The design of policies, economic and regulatory health care, should take into account barriers and facilitators of access as fundamental main points of health protection for migrants and, therefore, for the general population.

Qué pensar antes de decir que el paciente tiene un diagnóstico psiquiátrico. Parte I / What do you think before that you said: the patient has a psychiatric diagnosis. Part I

Resumen Los pacientes refieren sus síntomas en una gran variedad de términos como: "estoy cansado", "me duelen las articulaciones", "me pica todo el cuerpo", "tengo la boca seca", entre otros. Ante estos síntomas el médico piensa de manera automática en un número limitado de patologías que le son familiares, pero existen muchas otras causas a estos síntomas que no se tienen en cuenta. El desconocimiento del médico hace que en el paciente se genere inconformidad al no tenerse un diagnóstico correcto y un tratamiento adecuado, esto lleva a múltiples consultas y que el médico llegue a preguntarse a sí mismo "¿será que este paciente tiene un diagnóstico psiquiátrico?". En este artículo se enumeran las causas frecuentes de estos síntomas mencionados, se describen causas que son pocas veces sospechadas y las claves clínicas para que el médico pueda hacer el diagnóstico de éstas. La primera parte desarrollará los síntomas: fatiga, parestesias, prurito, artralgias, ansiedad y cambios en el comportamiento. La segunda parte desarrollará los síntomas: intolerancia a los alimentos, xerostomía, síncope, disfagia y manifestaciones en pacientes con cirugía bariátrica.

Abstract Patients refer their symptoms in a variety of terms such as: "I am tired", "my joints hurt", "my body itches", "my mouth is dry", among others. Given these symptoms, the doctor automatically thinks in a limited number of pathologies that are familiar to him, but there are many other causes to these symptoms that are not taken into account. The lack of knowledge of the doctor causes the patient to be dissatisfied by not having a correct diagnosis and adequate treatment, this leads to multiple visits and the doctor comes to ask himself "will this patient have a psychiatric diagnosis?". This article lists the frequent causes of these symptoms, describes causes that are rarely suspected and the clinical keys for the doctor to diagnose them. The first part will address the symptoms: fatigue, paresthesia, pruritus, arthralgia, anxiety and changes in behavior. The second part will develop the symptoms: intolerance to food, xerostomia, syncope, dysphagia and manifestations in patients with bariatric surgery.

Index of vulnerability of elderly people in Medellín, Barranquilla, and Pasto

Introduction: Vulnerability can be defined as a lack of material and immaterial resources, which prevents the use of opportunities that may advance one's self-interest. The presence of these welfare resources prevents reductions in the quality of life. Objective: The objective of this study was to build an index of vulnerability using characteristics of the physical, human, social and functional capital of adults in three cities of Colombia in the year 2016 and to determine the factors that contribute most to vulnerability. Materials and methods: We conducted a transversal study with primary information sources applying 1,514 surveys among people aged 60 years and over in Medellín, Barranquilla, and Pasto. For the construction of the vulnerability index, we used factor analysis with varimax rotation and the principal component method. Results: The conditions that lead to a person's vulnerability were related mainly to human capital (quality of life, mental health and habits). The other types of capital that contributed to vulnerability were physical capital (occupation), social capital (accompaniment), and functional capital (functional independence). The highest vulnerability was registered among the residents of Pasto. The factors associated with vulnerability were the city of residence, the sex, the educational level and the role of the person in the home. Conclusion: In 58.55% of elderly people vulnerability was explained by the use of time, the functional independence and the subjective well-being. These findings contribute to the improvement of the quality of life, mainly those related to maintaining functional independence as long as possible, being occupied, improving mental health, and avoiding the risks of depression, anxiety, cognitive deterioration and deleterious habits.

Índice de vulnerabilidad de adultos mayores en Medellín, Barranquilla y Pasto / Index of vulnerability of elderly people in Medellín, Barranquilla, and Pasto

Resumen Introducción. La vulnerabilidad puede entenderse como la carencia de recursos materiales e inmateriales que impide el aprovechamiento de oportunidades en distintos aspectos de la vida. Estos recursos de bienestar evitan el deterioro de la calidad de vida. Objetivo. Construir un índice de vulnerabilidad con las características de los capitales físico, humano, social y funcional de los adultos mayores de tres ciudades de Colombia en el 2016, y determinar los factores asociados con esta condición. Materiales y métodos. Se hizo un estudio transversal con información primaria mediante 1.514 encuestas a personas de 60 años omásde Medellín, Barranquilla y Pasto. En la construcción del índice se usó el análisis factorial con losmétodos de componentes principales y de rotación ortogonal varimax. Resultados. Las condiciones que generaban vulnerabilidad se relacionaron principalmente con el capital humano (calidad de vida, salud mental y hábitos); los demás capitales aportaron un solo componente, así: capital físico (ocupación), capital social (acompañamiento) y capital funcional (independencia funcional). La vulnerabilidad fue mayor en los residentes de Pasto. Los factores asociados con la vulnerabilidad fueron la ciudad de residencia, el sexo, el nivel educativo y el rol en el hogar. Conclusión. En el 58,55 % de las personas mayores, la vulnerabilidad se explicó por el uso del tiempo, la independencia funcional y el bienestar subjetivo. Estos hallazgos aportan elementos para el mejoramiento de la calidad de vida, principalmente en cuanto a la capacidad funcional para mantener la independencia, estar ocupados y fortalecer la salud mental.

Abstract Introduction: Vulnerability can be defined as a lack of material and immaterial resources, which prevents the use of opportunities that may advance one's self-interest. The presence of these welfare resources prevents reductions in the quality of life. Objective: The objective of this study was to build an index of vulnerability using characteristics of the physical, human, social and functional capital of adults in three cities of Colombia in the year 2016 and to determine the factors that contribute most to vulnerability. Materials and methods: We conducted a transversal study with primary information sources applying 1,514 surveys among people aged 60 years and over in Medellín, Barranquilla, and Pasto. For the construction of the vulnerability index, we used factor analysis with varimax rotation and the principal component method. Results: The conditions that lead to a person's vulnerability were related mainly to human capital (quality of life, mental health and habits). The other types of capital that contributed to vulnerability were physical capital (occupation), social capital (accompaniment), and functional capital (functional independence). The highest vulnerability was registered among the residents of Pasto. The factors associated with vulnerability were the city of residence, the sex, the educational level and the role of the person in the home. Conclusion: In 58.55% of elderly people vulnerability was explained by the use of time, the functional independence and the subjective well-being. These findings contribute to the improvement of the quality of life, mainly those related to maintaining functional independence as long as possible, being occupied, improving mental health, and avoiding the risks of depression, anxiety, cognitive deterioration and deleterious habits.

Biguanides sensitize leukemia cells to ABT-737-induced apoptosis by inhibiting mitochondrial electron transport.

Metformin displays antileukemic effects partly due to activation of AMPK and subsequent inhibition of mTOR signaling. Nevertheless, Metformin also inhibits mitochondrial electron transport at complex I in an AMPK-independent manner, Here we report that Metformin and rotenone inhibit mitochondrial electron transport and increase triglyceride levels in leukemia cell lines, suggesting impairment of fatty acid oxidation (FAO). We also report that, like other FAO inhibitors, both agents and the related biguanide, Phenformin, increase sensitivity to apoptosis induction by the bcl-2 inhibitor ABT-737 supporting the notion that electron transport antagonizes activation of the intrinsic apoptosis pathway in leukemia cells. Both biguanides and rotenone induce superoxide generation in leukemia cells, indicating that oxidative damage may sensitize toABT-737 induced apoptosis. In addition, we demonstrate that Metformin sensitizes leukemia cells to the oligomerization of Bak, suggesting that the observed synergy with ABT-737 is mediated, at least in part, by enhanced outer mitochondrial membrane permeabilization. Notably, Phenformin was at least 10-fold more potent than Metformin in abrogating electron transport and increasing sensitivity to ABT-737, suggesting that this agent may be better suited for targeting hematological malignancies. Taken together, our results suggest that inhibition of mitochondrial metabolism by Metformin or Phenformin is associated with increased leukemia cell susceptibility to induction of intrinsic apoptosis, and provide a rationale for clinical studies exploring the efficacy of combining biguanides with the orally bioavailable derivative of ABT-737, Venetoclax.

Was access to health care easy for immigrants in Spain? The perspectives of health personnel in Catalonia and Andalusia.

Until April 2012, all Spanish citizens were entitled to health care and policies had been developed at national and regional level to remove potential barriers of access, however, evidence suggested problems of access for immigrants. In order to identify factors affecting immigrants' access to health care, we conducted a qualitative study based on individual interviews with healthcare managers (n=27) and professionals (n=65) in Catalonia and Andalusia, before the policy change that restricted access for some groups. A thematic analysis was carried out. Health professionals considered access to health care "easy" for immigrants and similar to access for autochthons in both regions. Clear barriers were identified to enter the health system (in obtaining the health card) and in using services, indicating a mismatch between the characteristics of services and those of immigrants. Results did not differ among regions, except for in Catalonia, where access to care was considered harder for users without a health card, due to the fees charged, and in general, because of the distance to primary health care in rural areas. In conclusion, despite the universal coverage granted by the Spanish healthcare system and developed health policies, a number of barriers in access emerged that would require implementing the existing policies. However, the measures taken in the context of the economic crisis are pointing in the opposite direction, towards maintaining or increasing barriers.

Carcinoma epidermoide cutáneo invasivo a cráneo: reporte de un caso / Invasive squamous cell carcinoma to skull: A clinical case presentation / Carcinoma epidermóide cutâneo a crânio: relato de caso clínico

Dentro del grupo de cáncer cutáneo no melanoma (CCNM), el Carcinoma cutáneo de células escamosas (CE) representa el 25% siendo el segundo más frecuente, con una incidencia a lo largo de la vida del 7 y 11%. El Carcinoma Epidermoide (CE) es más agresivo que el Carcinoma basocelular (CBC). También pueden invadir estructuras profundas, causando significativa destrucción local. Presentamos el caso clínico de una mujer de 71 años que había sido previamente intervenida por diagnóstico anatomopatológico de carcinoma epidermoide de cuero cabelludo moderadamente diferenciado. Posteriormente presentó amplia recidiva local en zona frontal con invasión de diploe craneal y espacio epidural. Fue intervenida quirúrgicamente y el defecto secundario se reparó con colgajo e injertos. La biopsia confirmó bordes libres. Sin embargo un mes después, la paciente presentó invasión del cáncer a techo de la órbita. Se describe el tratamiento quirúrgico realizado por los servicios de Cirugía Plástica y Neurocirugía. Se reporta este caso clínico, ya que la incidencia de cáncer en la piel ha aumentado en los últimos años, por las mayores áreas expuestas al sol y mayor longevidad. Sin embargo su evolución es detenida la mayoría de las veces con un diagnóstico y tratamiento oportuno, aspectos con los que no contó la paciente, terminando en una excepcional invasión intracraneal, implicación poco frecuente en la práctica clínica.

Within non-melanoma skin cancer (NMSC) group, squamous cell carcinoma (SCC) represents 25%, with an incidence over life of 7 to 11%. Epidermoid Carcinnoma is more aggressive than basal cell carcinoma (BCC). It also can invade deep structures, causing significant local destruction. The case of a 71 years old woman, who was previously pathologically diagnosed with moderately differentiated epidermoid carcinoma in the scalp, is reported. There is a high rate of frontal recurrence with invasion to skull and epidural space. Surgery was performed and the secondary defect was repaired with flap and graft. Biopsy showed free edges . However after one month, the patient presented cancer invasion roof of the orbit. The surgical treatment by plastic surgery and neurosurgery is described. The incidence of skin cancer has increased in recent years, because of larger sun-exposed areas and increased longevity. However, its evolution is slowed down most of the times with early diagnosis and appropriate treatment, aspects to which the patient had not had access to, ending in exceptional intracranial invasion, rare implication in clinical practice.

No grupo de câncer de pele não melanoma, o carcinoma espinocelular cutâneo (CEC) é responsável por 25 % dos casos e o segundo mais comum, com uma incidência de 7 a 11 %. O CEC é mais agressivo do que o carcinoma basocelular (CBC), também podem invadir estruturas mais profundas, causando destruição local significativa. Relata-se o caso de uma mulher de 71 anos, intervinda cirurgicamente pelo diagnóstico patológico de moderamente diferenciado de carcinoma de células escamosas no couro cabeludo. Apresentou extensa recorrência local na frente posteriormente com invasão da cabeça e o espaço epidural. O defeito secundário foi feito com retalho e enxerto, tomou-se biopsia, confirmaram-se bordes livres pela patologia, porém um mês depois, a paciente presentou invasão do câncer para o teto da orbita. Faz se relato da cirurgia feita por Cirurgia Plástica e Neurocirurgia. A incidência de câncer de pele tem aumentado nos últimos anos, pelas maiores áreas expostas da pele, porém, sua evolução é detida com a avaliação e tratamento atual. O caso clinico apresenta um paciente com diagnóstico e tratamento tardio, com invasão na cabeça excepcional, situação pouco freqüente na pratica clínica.

Laser ablation-laser induced breakdown spectroscopy for the measurement of total elemental concentration in soils.

The performances of traditional laser-induced breakdown spectroscopy (LIBS) and laser ablation-LIBS (LA-LIBS) were compared by quantifying the total elemental concentration of potassium in highly heterogeneous solid samples, namely soils. Calibration curves for a set of fifteen samples with a wide range of potassium concentrations were generated. The LA-LIBS approach produced a superior linear response different than the traditional LIBS scheme. The analytical response of LA-LIBS was tested with a large set of different soil samples for the quantification of the total concentration of Fe, Mn, Mg, Ca, Na, and K. Results showed an acceptable linear response for Ca, Fe, Mg, and K while poor signal responses were found for Na and Mn. Signs of remaining matrix effects for the LA-LIBS approach in the case of soil analysis were found and discussed. Finally, some improvements and possibilities for future studies toward quantitative soil analysis with the LA-LIBS technique are suggested.

The automated cell: compound and environment screening system (ACCESS) for chemogenomic screening.

The automated cell, compound and environment screening system (ACCESS) was developed as an automated platform for chemogenomic research. In the yeast Saccharomyces cerevisiae, a number of genomic screens rely on the modulation of gene dose to determine the mode of action of bioactive compounds or the effects of environmental/compound perturbations. These and other phenotypic experiments have been shown to benefit from high-resolution growth curves and a highly automated controlled environment system that enables a wide range of multi-well assays that can be run over many days without any manual intervention. Furthermore, precise control of drug dosing, timing of drug exposure, and precise timing of cell harvesting at specific generation times are important for optimal results. Some of these benefits include the ability to derive fine distinctions between growth rates of mutant strains (1) and the discovery of novel compounds and drug targets (2). The automation has also enabled large-scale screening projects with over 100,000 unique compounds screened to date including a thousand genome-wide screens (3). The ACCESS system also has a diverse set of software tools to enable users to set up, run, annotate, and evaluate complex screens with minimal training.

Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae.

BACKGROUND: Iron-deficiency anemia is the most prevalent form of anemia world-wide. The yeast Saccharomyces cerevisiae has been used as a model of cellular iron deficiency, in part because many of its cellular pathways are conserved. To better understand how cells respond to changes in iron availability, we profiled the yeast genome with a parallel analysis of homozygous deletion mutants to identify essential components and cellular processes required for optimal growth under iron-limited conditions. To complement this analysis, we compared those genes identified as important for fitness to those that were differentially-expressed in the same conditions. The resulting analysis provides a global perspective on the cellular processes involved in iron metabolism. RESULTS: Using functional profiling, we identified several genes known to be involved in high affinity iron uptake, in addition to novel genes that may play a role in iron metabolism. Our results provide support for the primary involvement in iron homeostasis of vacuolar and endosomal compartments, as well as vesicular transport to and from these compartments. We also observed an unexpected importance of the peroxisome for growth in iron-limited media. Although these components were essential for growth in low-iron conditions, most of them were not differentially-expressed. Genes with altered expression in iron deficiency were mainly associated with iron uptake and transport mechanisms, with little overlap with those that were functionally required. To better understand this relationship, we used expression-profiling of selected mutants that exhibited slow growth in iron-deficient conditions, and as a result, obtained additional insight into the roles of CTI6, DAP1, MRS4 and YHR045W in iron metabolism. CONCLUSION: Comparison between functional and gene expression data in iron deficiency highlighted the complementary utility of these two approaches to identify important functional components. This should be taken into consideration when designing and analyzing data from these type of studies. We used this and other published data to develop a molecular interaction network of iron metabolism in yeast.

A unique and universal molecular barcode array.

Molecular barcode arrays allow the analysis of thousands of biological samples in parallel through the use of unique 20-base-pair (bp) DNA tags. Here we present a new barcode array, which is unique among microarrays in that it includes at least five replicates of every tag feature. The use of smaller dispersed replicate features dramatically improves performance versus a single larger feature and allows the correction of previously undetectable hybridization defects.

Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast.

Haploinsufficiency is defined as a dominant phenotype in diploid organisms that are heterozygous for a loss-of-function allele. Despite its relevance to human disease, neither the extent of haploinsufficiency nor its precise molecular mechanisms are well understood. We used the complete set of Saccharomyces cerevisiae heterozygous deletion strains to survey the genome for haploinsufficiency via fitness profiling in rich (YPD) and minimal media to identify all genes that confer a haploinsufficient growth defect. This assay revealed that approximately 3% of all approximately 5900 genes tested are haploinsufficient for growth in YPD. This class of genes is functionally enriched for metabolic processes carried out by molecular complexes such as the ribosome. Much of the haploinsufficiency in YPD is alleviated by slowing the growth rate of each strain in minimal media, suggesting that certain gene products are rate limiting for growth only in YPD. Overall, our results suggest that the primary mechanism of haploinsufficiency in yeast is due to insufficient protein production. We discuss the relevance of our findings in yeast to human haploinsufficiency disorders.

Chemogenomic profiling: identifying the functional interactions of small molecules in yeast.

We demonstrate the efficacy of a genome-wide protocol in yeast that allows the identification of those gene products that functionally interact with small molecules and result in the inhibition of cellular proliferation. Here we present results from screening 10 diverse compounds in 80 genome-wide experiments against the complete collection of heterozygous yeast deletion strains. These compounds include anticancer and antifungal agents, statins, alverine citrate, and dyclonine. In several cases, we identified previously known interactions; furthermore, in each case, our analysis revealed novel cellular interactions, even when the relationship between a compound and its cellular target had been well established. In addition, we identified a chemical core structure shared among three therapeutically distinct compounds that inhibit the ERG24 heterozygous deletion strain, demonstrating that cells may respond similarly to compounds of related structure. The ability to identify on-and-off target effects in vivo is fundamental to understanding the cellular response to small-molecule perturbants.

Functional profiling of the Saccharomyces cerevisiae genome.

Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.