Evaluating the utility of identity-by-descent segment numbers for relatedness inference via information theory and classification

Despite decades of methods development for classifying relatives in genetic studies, pairwise relatedness methods' recalls are above 90% only for first through third degree relatives. The top-performing approaches, which leverage identity-by-descent (IBD) segments, often use only kinship coefficients, while others, including ERSA, use the number of segments relatives share. To quantify the potential for using segment numbers in relatedness inference, we leveraged information theory measures to analyze exact (i.e., produced by a simulator) IBD segments from simulated relatives. Over a range of settings, we found that the mutual information between the relatives' degree of relatedness and a tuple of their kinship coefficient and segment number is on average 4.6% larger than between the degree and the kinship coefficient alone. We further evaluated IBD segment number utility by building a Bayes classifier to predict first through sixth degree relationships using different feature sets. When trained and tested with exact segments, the inclusion of segment numbers improves the recall by between 0.0028 and 0.030 for second through sixth degree relatives. However, the recalls improve by less than 0.018 per degree when using inferred segments, suggesting limitations due to IBD detection accuracy. Lastly, we compared our Bayes classifier that includes segment numbers with ERSA and IBIS and found comparable results, with the Bayes classifier and ERSA slightly outperforming each other across different degrees. Overall, this study shows that IBD segment numbers can improve relatedness inference but that errors from current SNP array-based detection methods yield dampened signals in practice.

Segment number threshold determines juvenile onset of germline cluster proliferation in Platynereis dumerilii

Many animals rely on sexual reproduction to propagate by using gametes (oocytes and sperm). Development of sexual characters and generation of gametes are tightly coupled with the growth of an organism. Platynereis dumerilii is a marine segmented worm which has been used to study germline development and gametogenesis. Platynereis has 4 Primordial Germ Cells (PGCs) that arise early in development and these cells are thought to give rise to germ cell clusters found across the body in the juvenile worms. The germ cell clusters eventually form the gametes. The stages of germline development and how the 4 PGCs become the numerous germ cell clusters are not well-documented in the juvenile stages. Platynereis, like other segmented worms, grows by adding new segments at its posterior end. The number of segments generally reflect the growth state of the worms and therefore is a useful and easily measurable growth state metric. To understand how growth correlates with development and gametogenesis, we investigated germline development across several developmental stages using germline/multipotency markers. We found that segment number predicted the state of germline development and the abundance of germline clusters. Additionally, we found that keeping worms short in segment number via changing external conditions or via amputations supported segment number threshold requirement for germline development. Finally, we asked if these clusters in Platynereis play a role in regeneration (as similar free-roaming cells are observed in Hydra and planarian regeneration) and found that the clusters were not required for regeneration in Platynereis, suggesting a strictly germline nature. Overall, these molecular analyses suggest a previously unidentified developmental transition dependent on the growth state in juvenile Platynereis when germline proliferation is substantially increased.

Clinical Factors for Predicting Neurophysiological Improvements Upon Extension and Flexion in Cervical Spondylotic Myelopathy Patients: A Retrospective Cohort Study

BackgroundCervical extension and flexion are generally thought to be harmful to CSM patients. Contrary to previous notions, a proportion of CSM patients presented DSSEP improvement upon extension and/or flexion. This study aims to determine the prediction criteria for DSSEP improvement upon extension and flexion with clinical and neutral-position imaging.MethodsCSM patients between 2015 and 2019 were retrospectively evaluated. The recorded outcomes were DSSEP changes upon extension and flexion, disease duration, modified Japanese Orthopedic Association (mJOA) score, gait impairment presence, weakness of upper limb muscles, and positive Hoffmann sign designation. The collection of MRI data included the compression ratio, the number of stenotic levels, the Mühle stenosis grade and disc degeneration stage of the most severe segment, and the presence of ligamentum flavum hypertrophy and intramedullary T2WI hyperintensity. Cervical alignment types were evaluated on plain cervical lateral radiographs.ResultsForty-nine patients were finally enrolled. Nine (18.4%) and 11 (22.4%) patients showed DSSEP improvement upon extension and flexion, respectively. Logistic regression analysis showed that an involved segment number ≤ 2 (P=0.018) and a straight/sigmoid cervical alignment (P=0.033) were significant criteria for predicting DSSEP improvement upon extension (probability: 85.7%). Mühle grade 3 (P=0.022) and disease duration ≤ 6 months (P=0.04) were significant criteria for predicting improvement upon flexion (probability: 85.7%).ConclusionsCervical extension and flexion might not necessarily cause deterioration and can even improve some CSM patients' neurological function at DSSEP examination. The involved segment number and cervical alignment were related to extension DSSEP improvement, while the stenosis grade and disease durations were related to flexion improvement. Our work suggests potential significance of educating CSM patients on maintaining individualized neck positions based on their clinical and radiographic findings.BaTrial registrationThe trial was retrospectively registered on April 30th, 2020 and the registration number is "[2020]151".

Extremal values on the Sombor index of trees

The Sombor index of a graph is defined as where denote the degree of the vertex in . In this article, we determine the extremal values of the Sombor index of trees with some given parameters, including matching number, pendant vertices, diameter, segment number, branching number, etc. The corresponding extremal trees are characterized completely.

A Size-Dependent Multiple-Loop Negative Feedback System Describes Biological Segment Formation Based on the Clock and Wavefront Mechanism

We proposed a new mathematical model for biological segment formation based on the clock and wavefront mechanism suggested in 1970s. Here, we chose an invertebrate, Enchytraeus japonensis, as a model animal and adopted multiple-loop negative feedback system based on its physiological features. We numerically showed the segment number of the model animal is autopoietically controlled by a size-dependent function. Additionally, we discussed two cases of the irregular oscillations by applying the biological conditions for abnormal development. The present model showed robustness under local noise perturbations like many other biological oscillators and qualitatively described unique development of the model animal. As a result, we suggested that a global interaction of chemical signals in the body can also drive “segmentation clock”.

PENGUNGKAPAN JUMLAH SEGMEN PASCA KONVERGENSI IFRS

The purpose of this study is to examine what extent of disclosure segmental reporting after IFRS convergence in Indonesia. The great value of this study is highlighted by the effort to empirically investigate the beginning impact of segmental disclosure standard to segment number. Descriptive analysis was used to describe changes of Line Of Business (LOB) segment, geographical segment, level of specificity number. The study consist of 32 Multinational company that listing in Indonesian Stock Exchange (ISE) at 2012-2017. Thus result show that number and types of segments reported decrease 4% for LOB and 2% for geographic segment and using more disaggregated at geographic level. Those findings about changing can help to lead an insight of segmental disclosure implementation in the future.