Predicting functional upstream open reading frames in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive.</p> <p>Results</p> <p>In this paper, a new computational approach to predicting functional uORFs in the yeast <it>Saccharomyces cerevisiae </it>is presented. Our approach is based on inductive logic programming and makes use of a novel combination of knowledge about biological conservation, Gene Ontology annotations and genes' responses to different conditions. Our method results in a set of simple and informative hypotheses with an estimated sensitivity of 76%. The hypotheses predict 301 further genes to have 398 novel functional uORFs. Three (<it>RPC11</it>, <it>TPK1</it>, and <it>FOL1</it>) of these 301 genes have been hypothesised, following wet-experiments, by a related study to have functional uORFs. A comparison with another related study suggests that eleven of the predicted functional uORFs from genes <it>LDB17</it>, <it>HEM3</it>, <it>CIN8</it>, <it>BCK2</it>, <it>PMC1</it>, <it>FAS1</it>, <it>APP1</it>, <it>ACC1</it>, <it>CKA2</it>, <it>SUR1</it>, and <it>ATH1 </it>are strong candidates for wet-lab experimental studies.</p> <p>Conclusions</p> <p>Learning based prediction of functional uORFs can be done with a high sensitivity. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help to elucidate the regulatory roles of uORFs.</p

Pregnancy related back pain, is it related to aerobic fitness? A longitudinal cohort study

<p>Abstract</p> <p>Background</p> <p>Low back pain with onset during pregnancy is common and approximately one out of three women have disabling pain. The pathogenesis of the pain condition is uncertain and there is no information on the role of physical fitness. Whether poorer physical conditioning is a cause or effect of back pain is also disputed and information from prospective studies needed.</p> <p>Methods</p> <p>A cohort of pregnant women, recruited from maternal health care centers in central Sweden, were examined regarding estimated peak oxygen uptake by cycle ergometer test in early pregnancy, reported physical activity prior to pregnancy, basic characteristics, back pain during pregnancy and back pain postpartum.</p> <p>Results</p> <p>Back pain during the current pregnancy was reported by nearly 80% of the women. At the postpartum appointment this prevalence was 40%. No association was displayed between estimated peak oxygen uptake and incidence of back pain during and after pregnancy, adjusted for physical activity, back pain before present pregnancy, previous deliveries, age and weight. A significant inverse association was found between estimated peak oxygen uptake and back pain intensity during pregnancy and a direct association post partum, in a fully adjusted multiple linear regression analysis.</p> <p>Conclusions</p> <p>Estimated peak oxygen uptake and reported physical activity in early pregnancy displayed no influence on the onset of subsequent back pain during or after pregnancy, where the time sequence support the hypothesis that poorer physical deconditioning is not a cause but a consequence of the back pain condition. The mechanism for the attenuating effect of increased oxygen uptake on back pain intensity is uncertain.</p

Substantial fat mass loss reduces low-grade inflammation and induces positive alteration in cardiometabolic factors in normal-weight individuals

( )The accumulation of fat, especially in visceral sites, is a significant risk factor for several chronic diseases with altered cardiometabolic homeostasis. We studied how intensive long-term weight loss and subsequent weight regain affect physiological changes, by longitudinally interrogating the lipid metabolism and white blood cell transcriptomic markers in healthy, normal-weight individuals. The current study examined 42 healthy, young (age: 27.5 +/- 4.0 years), normal-weight (body mass index, BMI: 23.4 +/- 1.7 kg/m(2)) female athletes, of which 25 belong to the weight loss and regain group (diet group), and 17 to the control group. Participants were evaluated, and fasting blood samples were drawn at three time points: at baseline (PRE); at the end of the weight loss period (MID: 21.1 +/- 3.1 weeks after PRE); and at the end of the weight regain period (POST: 18.4 +/- 2.9 weeks after MID). Following the weight loss period, the diet group experienced a similar to 73% reduction (similar to 0.69 kg) in visceral fat mass (false discovery rate, FDR <2.0 x 10(-16)), accompanied by anti-atherogenic effects on transcriptomic markers, decreased low-grade inflammation (e.g., as alpha(1)-acid glycoprotein (FDR = 3.08 x 10(-13)) and hs-CRP (FDR = 2.44 x 10(-3))), and an increase in functionally important anti-atherogenic high-density lipoprotein -associated metabolites (FDR <0.05). This occurred even though these values were already at favorable levels in these participants, who follow a fitness-lifestyle compared to age- and BMI-matched females from the general population (n = 58). Following the weight regain period, most of the observed beneficial changes in visceral fat mass, and meta bolomic and transcriptomic profiles dissipated. Overall, the beneficial anti-atherogenic effects of weight loss can be observed even in previously healthy, normal-weight individuals.Peer reviewe

Gait in Pregnancy-related Pelvic girdle Pain: amplitudes, timing, and coordination of horizontal trunk rotations

Walking is impaired in Pregnancy-related Pelvic girdle Pain (PPP). Walking velocity is reduced, and in postpartum PPP relative phase between horizontal pelvis and thorax rotations was found to be lower at higher velocities, and rotational amplitudes tended to be larger. While attempting to confirm these findings for PPP during pregnancy, we wanted to identify underlying mechanisms. We compared gait kinematics of 12 healthy pregnant women and 12 pregnant women with PPP, focusing on the amplitudes of transverse segmental rotations, the timing and relative phase of these rotations, and the amplitude of spinal rotations. In PPP during pregnancy walking velocity was lower than in controls, and negatively correlated with fear of movement. While patients’ rotational amplitudes were larger, with large inter-individual differences, spinal rotations did not differ between groups. In the patients, peak thorax rotation occurred earlier in the stride cycle at higher velocities, and relative phase was lower. The earlier results on postpartum PPP were confirmed for PPP during pregnancy. Spinal rotations remained unaffected, while at higher velocities the peak of thorax rotations occurred earlier in the stride cycle. The latter change may serve to avoid excessive spine rotations caused by the larger segmental rotations

The validity of rheumatoid arthritis diagnoses in Finnish biobanks

Objective The aim of this study was to determine the validity of rheumatoid arthritis (RA) diagnoses in patients participating in Finnish biobanks. Method We reviewed the electronic medical records of 500 Finnish biobank participants: 125 patients with at least one visit with a diagnosis of seropositive RA, 125 patients with at least one visit with a diagnosis of seronegative RA, and 250 age- and gender-matched controls. The patients were chosen from five different biobank hospitals in Finland. A rheumatologist reviewed the medical records to assess whether each patients' diagnosis was correct. The diagnosis was compared with the diagnostic codes in the Finnish Care Register for Health Care (CRHC) and special reimbursement data of the Social Insurance Institution of Finland. Results The positive predictive value (PPV) of CRHC diagnosis of RA (for seropositive and seronegative RA combined) was 0.82. For patients with a special reimbursement for anti-rheumatic medications for RA, the PPV was 0.89. The PPV was higher in patients with more than one visit. For one, two, five, and 10 visits, the PPV was 0.82, 0.85, 0.89, and 0.90, respectively, and for patients who also had the special reimbursement, the PPV was 0.89, 0.91, 0.93, and 0.94 for one, two, five, and 10 visits, respectively. In patients positive for anti-citrullinated protein antibodies, the PPV was 0.98. Conclusion These results demonstrate that the validity of RA diagnoses in Finnish biobanks was good and can be further improved by including data on special reimbursement for medication, number of visits, and serological data.Peer reviewe

The validity of rheumatoid arthritis diagnoses in Finnish biobanks

Objective The aim of this study was to determine the validity of rheumatoid arthritis (RA) diagnoses in patients participating in Finnish biobanks. Method We reviewed the electronic medical records of 500 Finnish biobank participants: 125 patients with at least one visit with a diagnosis of seropositive RA, 125 patients with at least one visit with a diagnosis of seronegative RA, and 250 age- and gender-matched controls. The patients were chosen from five different biobank hospitals in Finland. A rheumatologist reviewed the medical records to assess whether each patients' diagnosis was correct. The diagnosis was compared with the diagnostic codes in the Finnish Care Register for Health Care (CRHC) and special reimbursement data of the Social Insurance Institution of Finland. Results The positive predictive value (PPV) of CRHC diagnosis of RA (for seropositive and seronegative RA combined) was 0.82. For patients with a special reimbursement for anti-rheumatic medications for RA, the PPV was 0.89. The PPV was higher in patients with more than one visit. For one, two, five, and 10 visits, the PPV was 0.82, 0.85, 0.89, and 0.90, respectively, and for patients who also had the special reimbursement, the PPV was 0.89, 0.91, 0.93, and 0.94 for one, two, five, and 10 visits, respectively. In patients positive for anti-citrullinated protein antibodies, the PPV was 0.98. Conclusion These results demonstrate that the validity of RA diagnoses in Finnish biobanks was good and can be further improved by including data on special reimbursement for medication, number of visits, and serological data.Peer reviewe