The Integration Hypothesis: An Evolutionary Pathway to Benign SIV Infection

Untreated human immunodeficiency virus (HIV) infection in humans is typically characterised by persistent high virus load, failure of the immune response to clear the virus, and fatal disease outcome. Natural hosts of closely related simian immunodeficiency viruses (SIVs)—e.g., sooty mangabeys [1,2]—maintain comparably high persistent virus levels and yet remain healthy

How Universal is Genre in Universal Dependencies?

This work provides the first in-depth analysis of genre in Universal Dependencies (UD). In contrast to prior work on genre identification which uses small sets of well-defined labels in mono-/bilingual setups, UD contains 18 genres with varying degrees of specificity spread across 114 languages. As most treebanks are labeled with multiple genres while lacking annotations about which instances belong to which genre, we propose four methods for predicting instance-level genre using weak supervision from treebank metadata. The proposed methods recover instance-level genre better than competitive baselines as measured on a subset of UD with labeled instances and adhere better to the global expected distribution. Our analysis sheds light on prior work using UD genre metadata for treebank selection, finding that metadata alone are a noisy signal and must be disentangled within treebanks before it can be universally applied.Comment: Accepted at SyntaxFest 202

Subspace Chronicles: How Linguistic Information Emerges, Shifts and Interacts during Language Model Training

Representational spaces learned via language modeling are fundamental to Natural Language Processing (NLP), however there has been limited understanding regarding how and when during training various types of linguistic information emerge and interact. Leveraging a novel information theoretic probing suite, which enables direct comparisons of not just task performance, but their representational subspaces, we analyze nine tasks covering syntax, semantics and reasoning, across 2M pre-training steps and five seeds. We identify critical learning phases across tasks and time, during which subspaces emerge, share information, and later disentangle to specialize. Across these phases, syntactic knowledge is acquired rapidly after 0.5% of full training. Continued performance improvements primarily stem from the acquisition of open-domain knowledge, while semantics and reasoning tasks benefit from later boosts to long-range contextualization and higher specialization. Measuring cross-task similarity further reveals that linguistically related tasks share information throughout training, and do so more during the critical phase of learning than before or after. Our findings have implications for model interpretability, multi-task learning, and learning from limited data.Comment: Accepted at EMNLP 2023 (Findings

Establishing Trustworthiness: Rethinking Tasks and Model Evaluation

Language understanding is a multi-faceted cognitive capability, which the Natural Language Processing (NLP) community has striven to model computationally for decades. Traditionally, facets of linguistic intelligence have been compartmentalized into tasks with specialized model architectures and corresponding evaluation protocols. With the advent of large language models (LLMs) the community has witnessed a dramatic shift towards general purpose, task-agnostic approaches powered by generative models. As a consequence, the traditional compartmentalized notion of language tasks is breaking down, followed by an increasing challenge for evaluation and analysis. At the same time, LLMs are being deployed in more real-world scenarios, including previously unforeseen zero-shot setups, increasing the need for trustworthy and reliable systems. Therefore, we argue that it is time to rethink what constitutes tasks and model evaluation in NLP, and pursue a more holistic view on language, placing trustworthiness at the center. Towards this goal, we review existing compartmentalized approaches for understanding the origins of a model's functional capacity, and provide recommendations for more multi-faceted evaluation protocols.Comment: Accepted at EMNLP 2023 (Main Conference), camera-read

3-nitroimidazo[1,2-b]pyridazine as a novel scaffold for antiparasitics with sub-nanomolar anti-Giardia lamblia activity.

As there is a continuous need for novel anti-infectives, the present study aimed to fuse two modes of action into a novel 3-nitroimidazo[1,2-b]pyridazine scaffold to improve antiparasitic efficacy. For this purpose, we combined known structural elements of phosphodiesterase inhibitors, a target recently proposed for Trypanosoma brucei and Giardia lamblia, with a nitroimidazole scaffold to generate nitrosative stress. The compounds were evaluated in vitro against a panel of protozoal parasites, namely Giardia lamblia, Trypanosoma brucei, T. cruzi, Leishmania infantum and Plasmodium falciparum and for cytotoxicity on MRC-5 cells. Interestingly, selective sub-nanomolar activity was obtained against G. lamblia, and by testing several analogues with and without the nitro group, it was shown that the presence of a nitro group, but not PDE inhibition, is responsible for the low IC50 values of these novel compounds. Adding the favourable drug-like properties (low molecular weight, cLogP (1.2-4.1) and low polar surface area), the key compounds from the 3-nitroimidazo[1,2-b]pyridazine series can be considered as valuable hits for further anti-giardiasis drug exploration and development

Global plate motion frames: Toward a unified model

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94772/1/rog1664.pd

Is gene activity in plant cells affected by UMTS-irradiation? A whole genome approach

Mobile phone technology makes use of radio frequency (RF) electromagnetic fields transmitted through a dense network of base stations in Europe. Possible harmful effects of RF fields on humans and animals are discussed, but their effect on plants has received little attention. In search for physiological processes of plant cells sensitive to RF fields, cell suspension cultures of Arabidopsis thaliana were exposed for 24 h to a RF field protocol representing typical microwave exposition in an urban environment. mRNA of exposed cultures and controls was used to hybridize Affymetrix-ATH1 whole genome microarrays. Differential expression analysis revealed significant changes in transcription of 10 genes, but they did not exceed a fold change of 2.5. Besides that 3 of them are dark-inducible, their functions do not point to any known responses of plants to environmental stimuli. The changes in transcription of these genes were compared with published microarray datasets and revealed a weak similarity of the microwave to light treatment experiments. Considering the large changes described in published experiments, it is questionable if the small alterations caused by a 24 h continuous microwave exposure would have any impact on the growth and reproduction of whole plants