Salix shrub encroachment along a 1000 m elevation gradient triggers a major ecosystem change in the European Alps

Shrub encroachment, a globally recognized response to climate warming, usually involves late successional species in mountain environments, without alteration to climax communities. We show that a major ecosystem change is occurring in the European Alps across a 1000 m elevation gradient, with pioneer hygrophilous Salix shrubs, previously typical of riparian forests, wetlands and avalanche ravines, encroaching into the climax communities of subalpine and alpine belts shrublands and grasslands, as well as snowbeds, pioneer vegetation and barren grounds in the nival belt. We analyzed Salix recruitment through dendrochronological methods, and assessed its relationships with climate and atmospheric CO2 concentration. The dendrochronological data indicated that Salix encroachment commenced in the 1950s (based on the age of the oldest Salix individuals, recruited in 1957), and that it was correlated with increasing atmospheric CO2 concentration, spring warming and snow cover decrease. Hygrophilous Salix shrubs are expanding their distribution both through range filling and upwards migration, likely achieving competitive replacement of species of subalpine and alpine climax communities. They benefit from climate warming and CO2 fertilization and are not sensitive to spring frost damage and soil limitations, being observed across a gradient of soil conditions from loose glacial sediments in recently deglaciated areas (where soils had not had sufficient time to develop) to mature soils such as podzols (when colonizing late successional subalpine shrublands). Salix encroachment may trigger ecosystem and landscape transformations, promoting the development of forests that replace pre-existing subalpine shrublands, and of open woodlands invading alpine grasslands and snowbeds, making the alpine environment similar to sub-Arctic and Arctic areas. This results in a new threat to the conservation of the plant species, communities and landscapes typical of the alpine biota, as mountain ranges such as the Alps provide limited opportunities for upward migration and range-shift

12-Month progression of motor and functional outcomes in congenital myotonic dystrophy

Background: We aim to describe 12-mo functional and motor outcome performance in a cohort of participants with congenital myotonic dystrophy (CDM). Methods: CDM participants performed the 6 Minute Walk Test (6MWT), 10 Meter Run, 4 Stair Climb, Grip Strength, and Lip Force at baseline and 12-mo visits. Parents completed the Vineland Adaptive Behavior Scale. Results: Forty-seven participants, aged 0 to 13 y old, with CDM were enrolled. 6MWT, 10 Meter Run, and 4 Stair Climb were completed in \u3e85% of eligible participants. The only significant difference between mean baseline and 12-mo performance was an improvement in 6MWT in children 3-6 y old (P =.008). This age group also had the largest mean % improvement in performance in all other timed functional testing. In children \u3e7 y, the slope of change on timed functional tests decreased or plateaued, with further reductions in performance in children ≥10 y. Participants with CTG repeat lengths \u3c500 did not perform differently than those with repeat lengths \u3e1000. Conclusions: The 6MWT, 10 Meter Run, and 4 Stair Climb were the most feasible measures. Our findings are consistent with the clinical profile and prior cross-sectional data, helping to establish reasonable expectations of functional trajectories in this population as well as identifying points in which therapeutic interventions may be best studied. Further study of outcomes in children \u3e10 y old and \u3c3 y is warranted, but this new information will assist planning of clinical trials in the CDM population

ABEMUS: platform specific and data informed detection of somatic SNVs in cfDNA

MOTIVATION: The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single nucleotide variants (SNVs) in circulating cell free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs. RESULTS: We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples. AVAILABILITY: ABEMUS is cross-platform and can be installed as R package. The source code is maintained on Github at http://github.com/cibiobcg/abemus and it is also available at CRAN official R repository. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

The promises of large language models for protein design and modeling.

The recent breakthroughs of Large Language Models (LLMs) in the context of natural language processing have opened the way to significant advances in protein research. Indeed, the relationships between human natural language and the language of proteins invite the application and adaptation of LLMs to protein modelling and design. Considering the impressive results of GPT-4 and other recently developed LLMs in processing, generating and translating human languages, we anticipate analogous results with the language of proteins. Indeed, protein language models have been already trained to accurately predict protein properties, generate novel functionally characterized proteins, achieving state-of-the-art results. In this paper we discuss the promises and the open challenges raised by this novel and exciting research area, and we propose our perspective on how LLMs will affect protein modeling and design

The promises of large language models for protein design and modeling

The recent breakthroughs of Large Language Models (LLMs) in the context of natural language processing have opened the way to significant advances in protein research. Indeed, the relationships between human natural language and the “language of proteins” invite the application and adaptation of LLMs to protein modelling and design. Considering the impressive results of GPT-4 and other recently developed LLMs in processing, generating and translating human languages, we anticipate analogous results with the language of proteins. Indeed, protein language models have been already trained to accurately predict protein properties, generate novel functionally characterized proteins, achieving state-of-the-art results. In this paper we discuss the promises and the open challenges raised by this novel and exciting research area, and we propose our perspective on how LLMs will affect protein modeling and design

An expectation-maximization framework for comprehensive prediction of isoform-specific functions.

MOTIVATION: Advances in RNA sequencing technologies have achieved an unprecedented accuracy in the quantification of mRNA isoforms, but our knowledge of isoform-specific functions has lagged behind. There is a need to understand the functional consequences of differential splicing, which could be supported by the generation of accurate and comprehensive isoform-specific gene ontology annotations. RESULTS: We present isoform interpretation, a method that uses expectation-maximization to infer isoform-specific functions based on the relationship between sequence and functional isoform similarity. We predicted isoform-specific functional annotations for 85 617 isoforms of 17 900 protein-coding human genes spanning a range of 17 430 distinct gene ontology terms. Comparison with a gold-standard corpus of manually annotated human isoform functions showed that isoform interpretation significantly outperforms state-of-the-art competing methods. We provide experimental evidence that functionally related isoforms predicted by isoform interpretation show a higher degree of domain sharing and expression correlation than functionally related genes. We also show that isoform sequence similarity correlates better with inferred isoform function than with gene-level function. AVAILABILITY AND IMPLEMENTATION: Source code, documentation, and resource files are freely available under a GNU3 license at https://github.com/TheJacksonLaboratory/isopretEM and https://zenodo.org/record/7594321

Evaluation and predictive modeling of shelf life of minced beef meat stored in high-oxygen modified atmosphere packaging at different temperatures

The aims were: (1) to follow the freshness decay of minced beef stored in high-oxygen modified atmosphere packaging at different temperatures (4.3, 8.1 and 15.5 \ub0C) by applying traditional methods (microbiological counts, color evaluation, thiobarbituric acid assay TBA, headspace gas composition) and e-nose; (2) to model the decay kinetics to obtain information about the maximum shelf life as function of storage conditions. The minced beef, packaged in modified atmosphere was supplied by a manufacturer at the beginning of its commercial life. The study demonstrated the ability of the traditional methods to describe the kinetics of freshness decay. The modeling of the experimental data and the comparison with microbiological or chemical thresholds allowed the setting, for each index, of a stability time above which the meat was no longer acceptable. The quality decay of meat was also evaluated by the headspace fingerprint of the same set of samples by means of a commercial e-nose. A clear discrimination between \u201cfresh\u201d and \u201cold\u201d samples was obtained using PCA and CA, determining at each temperature a specific range of stability time. The mean value of the stability times calculated for each index was 9 days at 4.3 \ub0C (recommended storage temperature), 3\u20134 days at 8.1 \ub0C (usual temperature in household refrigerators) and 2 days at 15.5 \ub0C (abuse temperature). Resolution of the stability times allowed calculation of mean Q10 values, i.e. the increase in rate for a 10 \ub0C increase in temperature. The results show that the Q10 values from the traditional methods (3.6\u20134.0 range) overlapped with those estimated with e-nose and color indexes (3.4 and 3.9, respectively)

A three-dimensional study of body motion during ergometer rowing

Abstract: Background: Rowing movements can be simulated using specialized ergometers; the method can be used both for training and indoor assessment of body movements within controlled conditions. Purpose: To perform a three-dimensional quantitative analysis of body movements during ergometer rowing, and to examine if there is a relationship between anthropometry and rowing kinematics. Study Design: Descriptive Laboratory Study Methods: Body movements were recorded in 18 high-level oarsmen during ergometer rowing at 28 strokes/min. The three-dimensional movements of 21 body landmarks (left and right ankle, knee, greater trochanter, hip, shoulder, elbow, wrist, tragus; spinous process of C7, T2, T12, L2, L4) were detected by an optoelectronic instrument. Using dedicated software\ub8 the range of motion of the posterior angles of the cervical, thoracic and lumbar spine segments relative to the horizontal axis; the angles between greater trochanter- knee- ankle and between knee-ankle and the ground; head rotation and tilt; leg and upper limb symmetry, were computed. Results: The head and neck were approximately in line with the horizontal at catch, and extended at finish, with limited horizontal and frontal plane inclinations. Thoracic spine extension during the stroke was on average 68\ub0. Lumbar spine range of motion was on average 59\ub0, and it was smaller in weightier oarsmen. Upper limbs were symmetric, and a complete, symmetric extension of the lower limbs was made. At catch the legs were nearly perpendicular to the ground. Conclusions: The method allowed the measurement of the kinematic characteristics of the body during ergometer rowing. The measurements agreed with conventional technical teaching. Clinical Relevance: Data collected on high-level rowers can provide a set of standard quantitative execution parameters that can be used by coaches as a benchmark for the assessment of technical movements in all rowers

Raman spectroscopy of graphene and bilayer under biaxial strain: bubbles and balloons

In this letter we use graphene bubbles to study the Raman spectrum of graphene under biaxial (e.g. isotropic) strain. Our Gruneisen parameters are in excellent agreement with the theoretical values. Discrepancy in the previously reported values is attributed to the interaction of graphene with the substrate. Bilayer balloons (intentionally pressurized membranes) have been used to avoid the effect of the substrate and to study the dependence of strain on the inter-layer interactions.Comment: 14 pages, 4 figure