Coupled Two-Way Clustering Analysis of Gene Microarray Data

We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant partitions emerge. The search for such subsets is a computationally complex task: we present an algorithm, based on iterative clustering, which performs such a search. This analysis is especially suitable for gene microarray data, where the contributions of a variety of biological mechanisms to the gene expression levels are entangled in a large body of experimental data. The method was applied to two gene microarray data sets, on colon cancer and leukemia. By identifying relevant subsets of the data and focusing on them we were able to discover partitions and correlations that were masked and hidden when the full dataset was used in the analysis. Some of these partitions have clear biological interpretation; others can serve to identify possible directions for future research

Investigating the Minimal Counterintuitiveness Effect

Scholars believe that minimally counterintuitive concepts are more memorable than intuitive ones (Barrett, 2008; Upal 2011). If an item has an unusual or counterintuitive property, such as a ball that rises rather than falls when dropped, the unusual property makes the item more memorable. However, experiments investigating this effect tend to have experimental confounds that make interpretation difficult. Our experiment aimed to solve these problems by using counterbalanced lists of nonwords, using the nonwords to control for prior associations and experiences. Participants viewed a series of nonwords along with a noun-adjective pair (e.g. Frav – a roaring tiger) and were told that each nonword represented a name. Some nonwords were the names of an intuitive item (e.g. a roaring tiger) whereas others were counterintuitive (e.g. a writing tiger). Participants rated the likelihood that the described nonword was from Earth or from a parallel universe where things were different. Everyone was told to remember the nonwords and noun-adjective pairs for a later test. To improve overall recall, each item was presented and rated twice. After a distractor, participants were asked to recall as many of the nonwords as possible. The results revealed that counterintuitive items were not better-recalled than intuitive items. In fact, in most tests, intuitive items were recalled significantly more often than intuitive items. Our results do not support the Minimal Counterintuitiveness Effect and suggest that when to-be-remembered words and their accompanying nouns are matched across conditions (counterintuitive and intuitive), that intuitive information is more memorable than counterintuitive information

Cardiovascular and metabolic responses during indoor climbing and laboratory cycling exercise in advanced and élite climbers

Purpose. To validate heart rate (fH) as an effective indicator of the aerobic demands of climbing, the fH vs. oxygen uptake (VO2) relationship determined during cycling exercise and climbing on a circular climbing treadwall was compared. Possible differences in maximum aerobic characteristics between advanced and \ue9lite climbers were also assessed. Methods. Seven advanced and six \ue9lite climbers performed a discontinuous incremental test on a cycle ergometer and a similar test on a climbing treadwall. Cardiorespiratory and gas exchange parameters were collected at rest and during exercise. Results. The fH vs. VO2 relationship was steeper during cycling than climbing at submaximal exercise for both groups and during climbing in the \ue9lite climbers as compared to the advanced. At peak exercise, VO2 was similar during both cycling and climbing (3332\ub1115 and 3193\ub1129 ml/min, respectively). Despite similar VO2 peak, the \ue9lite climbers had a higher peak workload during climbing (11.8\ub10.8 vs. 9.2\ub10.3 m/min in \ue9lite and advanced climbers, respectively; P=.024) but not during cycling (282\ub113 vs. 268\ub112 W in \ue9lite and advanced climbers, respectively). Conclusions. Our findings indicate that care should be taken when energy expenditure during climbing is estimated from the fH vs VO2 relationship determined in the laboratory. The level of climbing experience significantly affects the energy cost of exercise. Lastly, the similar aerobic demands of cycling and climbing at peak exercise, suggest that maximum VO2 may play an important role in climbing performance. Specific training methodologies should be implemented to improve aerobic power in climbers

Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens

Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding and shotgun metagenomics could be used to simultaneously detect all known pathogens and potentially new ones. This review aims to present the current status of high-throughput sequencing (HTS) diagnostics of fungal and bacterial plant pathogens, discuss the challenges that need to be addressed, and provide direction for the development of methods for the detection of a restricted number of related taxa (specific surveillance) or all of the microorganisms present in a sample (general surveillance). HTS techniques, particularly metabarcoding, could be useful for the surveillance of soilborne, seedborne and airborne pathogens, as well as for identifying new pathogens and determining the origin of outbreaks. Metabarcoding and shotgun metagenomics still suffer from low precision, but this issue can be limited by carefully choosing primers and bioinformatic algorithms. Advances in bioinformatics will greatly accelerate the use of metagenomics to address critical aspects related to the detection and surveillance of plant pathogens in plant material and foodstuffs

Effects of in-season enhanced negative work-based vs traditional weight training on change of direction and hamstrings-to-quadriceps ratio in soccer players

The present study investigated the effects of in-season enhanced negative work-based training (ENT) vs weight training in the change of direction (COD), sprinting and jumping ability, muscle mass and strength in semi-professional soccer players. Forty male soccer players participated in the eight-week, 1 d/w intervention consisting of 48 squat repetitions for ENT using a flywheel device (inertia=0.11 kg\ub7m-2) or weight training (80%1 RM) as a control group (CON). Agility T-test, 20+20 m shuttle, 10 m and 30 m sprint, squat jump (SJ) and countermovement jump (CMJ), lean mass, quadriceps and hamstrings strength and the hamstrings-to-quadriceps ratio were measured. Time on agility T-test and 20+20 m shuttle decreased in ENT (effect-size =-1.44, 95% CI -2.24/-0.68 and -0.75, -1.09/-0.42 respectively) but not in CON (-0.33, -0.87/0.19 and -0.13, -0.58/0.32). SJ and CMJ height increased in both ENT (0.71, 0.45/0.97 and 0.65, 0.38/0.93) and CON (0.41, 0.23/0.60 and 0.36, 0.12/0.70). Overall, quadriceps and hamstrings strength increased in both ENT and CON (0.38/0.79), but the hamstrings-to-quadriceps ratio increased in ENT (0.31, 0.22/0.40) but not in CON (0.03, -0.18/0.24). Lean mass increased in both ENT (0.41, 0.26/0.57) and CON (0.29, 0.14/0.44). The repeated negative actions performed in ENT may have led to improvements in braking ability, a key point in COD performance. Semiprofessional soccer players may benefit from in-season ENT to enhance COD and the negative-specific adaptations in muscle strength and hamstrings-to-quadriceps ratio

New perspectives in the prediction of postoperative complications for high-risk ulcerative colitis patients: machine learning preliminary approach

OBJECTIVE: Patients with acute severe and medical refractory ulcerative colitis have a high risk of postoperative complications after total abdominal colectomy (TAC). The objective of this retrospective study is to use machine learning to analyze and predict short-term outcomes. PATIENTS AND METHODS: 32 patients with ulcerative colitis were treated with total abdominal colectomy between 2011 and 2017. Biographical data, preoperative therapy, blood chemistry, nutritional status, surgical technique, blood transfusion and preoperative length of stay were the features selected for the statistical analyses and were used as input for the machine learning algorithms to predict the rate of complications. RESULTS: Traditional statistical analysis showed an overall postoperative morbidity rate of 34% and a mortality rate of 3%. Preoperative low serum albumin levels (4 days), blood transfusions (≥1 unit) and body temperature (≥37.5°C) demonstrated a major impact on infectious morbidity with statistical significance (p<0.05). Patients treated with steroids and rescue therapy presented a higher risk of minor infectious complications (p<0.05). Evaluating only preoperative features, machine learning algorithms were able to predict minor postoperative complications with a high strike rate (84.3%), high sensitivity (87.5%) and high specificity (83.3%) during the testing phase. CONCLUSIONS: Machine learning is demonstrated to be useful in predicting the rate of minor postoperative complications in high-risk ulcerative colitis patients, despite the small sample size. It represents a major step forward in data analysis by implementing a retrospective study from a prospective point of view

Management of the mother-infant dyad with suspected or confirmed SARS-CoV-2 infection in a highly epidemic context

In the context of SARS-CoV-2 pandemic, the hospital management of mother-infant pairs poses to obstetricians and neonatologists previously unmet challenges. In Lombardy, Northern Italy, 59 maternity wards networked to organise the medical assistance of mothers and neonates with suspected or confirmed SARS-CoV-2 infection. Six "COVID-19 maternity centres" were identified, the architecture and activity of obstetric and neonatal wards of each centre was reorganised, and common assistance protocols for the management of suspected and proven cases were formulated. Here, we present the key features of this reorganization effort, and our current management of the mother-infant dyad before and after birth, including our approach to rooming-in practice, breastfeeding and neonatal follow-up, based on the currently available scientific evidence. Considered the rapid diffusion of COVID-19 all over the world, we believe that preparedness is fundamental to assist mother-infant dyads, minimising the risk of propagation of the infection through maternity and neonatal wards

The IgA nephropathy Biobank. An important starting point for the genetic dissection of a complex trait

BACKGROUND: IgA nephropathy (IgAN) or Berger's disease, is the most common glomerulonephritis in the world diagnosed in renal biopsied patients. The involvement of genetic factors in the pathogenesis of the IgAN is evidenced by ethnic and geographic variations in prevalence, familial clustering in isolated populations, familial aggregation and by the identification of a genetic linkage to locus IGAN1 mapped on 6q22–23. This study seems to imply a single major locus, but the hypothesis of multiple interacting loci or genetic heterogeneity cannot be ruled out. The organization of a multi-centre Biobank for the collection of biological samples and clinical data from IgAN patients and relatives is an important starting point for the identification of the disease susceptibility genes. DESCRIPTION: The IgAN Consortium organized a Biobank, recruiting IgAN patients and relatives following a common protocol. A website was constructed to allow scientific information to be shared between partners and to divulge obtained data (URL: ). The electronic database, the core of the website includes data concerning the subjects enrolled. A search page gives open access to the database and allows groups of patients to be selected according to their clinical characteristics. DNA samples of IgAN patients and relatives belonging to 72 multiplex extended pedigrees were collected. Moreover, 159 trios (sons/daughters affected and healthy parents), 1068 patients with biopsy-proven IgAN and 1040 healthy subjects were included in the IgAN Consortium Biobank. Some valuable and statistically productive genetic studies have been launched within the 5(th )Framework Programme 1998–2002 of the European project No. QLG1-2000-00464 and preliminary data have been published in "Technology Marketplace" website: . CONCLUSION: The first world IgAN Biobank with a readily accessible database has been constituted. The knowledge gained from the study of Mendelian diseases has shown that the genetic dissection of a complex trait is more powerful when combined linkage-based, association-based, and sequence-based approaches are performed. This Biobank continuously expanded contains a sample size of adequately matched IgAN patients and healthy subjects, extended multiplex pedigrees, parent-child trios, thus permitting the combined genetic approaches with collaborative studies

Specific adaptations in performance and muscle architecture after weighted jump-squat vs body mass squat jump training in recreational soccer players

The aim of the present study was to compare the effects of weighted jump squat (WJST) vs body mass squat jump training (BMSJT) on quadriceps muscle architecture, lower-limb lean-mass (LM) and muscle strength, performance in change of direction (COD), sprint and jump in recreational soccer-players. Forty-eight healthy soccer-players participated in an off-season randomized controlled-trial. Before and after an eight-week training intervention, vastus lateralis pennation angle, fascicle length, muscle thickness, LM, squat 1-RM, quadriceps and hamstrings isokinetic peak-torque, agility T-test, 10 and 30m sprint and squat-jump (SJ) were measured. Although similar increases in muscle thickness, fascicle length increased more in WJST (ES=1.18, 0.82-1.54) than in BMSJT (ES=0.54, 0.40-0.68) and pennation angle only increased in BMSJT (ES=1.03, 0.78-1.29). Greater increases in LM were observed in WJST (ES=0.44, 0.29-0.59) than in BMSJT (ES=0.21, 0.07-0.37). Agility T-test (ES=2.95, 2.72-3.18), 10m (ES=0.52, 0.22-0.82) and 30m-sprint (ES=0.52, 0.23-0.81) improved only in WJST, while SJ improved in BMSJT (ES=0.89, 0.43-1.35) more than in WJST (ES=0.30, 0.03-0.58). Similar increases in squat 1-RM and peak-torque occurred in both groups. The greater inertia accumulated within the landing-phase in WJST vs BMSJT has increased the eccentric workload, leading to specific eccentric-like adaptations in muscle architecture. The selective improvements in COD in WJST may be related to the increased braking ability generated by the enhanced eccentric workload