Miracle-dz/UniFAR-FTUs huggingface dataset:
Image Segmentation for Fruit Detection and Yield Estimation in Apple Orchards

Ground vehicles equipped with monocular vision systems are a valuable source of high‐resolution image data for precision agriculture applications in orchards. This paper presents an image processing framework for fruit detection and counting using orchard image data. A general‐purpose image segmentation approach is used, including two feature learning algorithms; multiscale multilayered perceptrons (MLP) and convolutional neural networks (CNN). These networks were extended by including contextual information about how the image data was captured (metadata), which correlates with some of the appearance variations and/or class distributions observed in the data. The pixel‐wise fruit segmentation output is processed using the watershed segmentation (WS) and circular Hough transform (CHT) algorithms to detect and count individual fruits. Experiments were conducted in a commercial apple orchard near Melbourne, Australia. The results show an improvement in fruit segmentation performance with the inclusion of metadata on the previously benchmarked MLP network. We extend this work with CNNs, bringing agrovision closer to the state‐of‐the‐art in computer vision, where although metadata had negligible influence, the best pixel‐wise F1‐score of 0.791 was achieved. The WS algorithm produced the best apple detection and counting results, with a detection F1‐score of 0.861. As a final step, image fruit counts were accumulated over multiple rows at the orchard and compared against the post‐harvest fruit counts that were obtained from a grading and counting machine. The count estimates using CNN and WS resulted in the best performance for this data set, with a squared correlation coefficient of r2=0.826 .
Multifocal systemic tuberculosis: the many faces of an old nemesis.

BACKGROUND Tuberculosis continues to be a major health problem, where an estimated 7-8 million new cases are diagnosed each year. Multifocal tuberculosis is characterized by the presence of large multifocal tuberculous areas in the same or different organs. Difficulty in diagnosis of multifocal tuberculosis and consideration of other diseases may lead to a delay in diagnosing this entity. Here the clinical features and characteristics of three patients with multifocal systemic tuberculosis are described. CASE REPORT During the period of 1999-2005, a total of 128 confirmed cases of tuberculosis were identified. Three (2.3%) patients had multifocal systemic tuberculosis. The first case had involvement of the lung, psoas muscle, and the vertebral bodies. The second patient had multiple brain lesions with mediastinal and retroperitoneal lymphadenopathy. The third patient had multiple brain lesions, lymphadenopathy, and colonic lesions initially mimicking a metastatic disease. Mycobacterium tuberculosis was grown from pleural fluid in one patient and from lymph node biopsies in another patient. The third patient had histopathologic evidence of tuberculosis. All patients received standard anti-tuberculous treatment, resulting in a full recovery in two patients, while the third patient had residual weakness. CONCLUSIONS Multifocal systemic tuberculosis may pose a diagnostic challenge and may occur in immunocompetent hosts, in whom this entity generally has a good outcome.
Cosmology and cluster halo scaling relations

We explore the effects of dark matter and dark energy on the dynamical scaling properties of galaxy clusters. We investigate the cluster Faber-Jackson (FJ), Kormendy and Fundamental Plane (FP) relations between the mass, radius and velocity dispersion of cluster-sized haloes in cosmological N-body simulations. The simulations span a wide range of cosmological parameters, representing open, flat and closed Universes. Independently of the cosmology, we find that the simulated clusters are close to a perfect virial state and do indeed define an FP. The fitted parameters of the FJ, Kormendy and FP relationships do not show any significant dependence on (m) and/or (Lambda). One outstanding effect is the influence of (m) on the thickness of the FP. Following the time evolution of our models, we find slight changes of FJ and Kormendy parameters in high-(m) universe, along with a slight decrease of FP fitting parameters. We also see an initial increase of the FP thickness followed by a convergence to a nearly constant value. The epoch of convergence is later for higher values of (m), while the thickness remains constant in the low-(m) Lambda models. We also find a continuous increase of the FP thickness in the standard cold dark matter cosmology. There is no evidence that these differences are due to the different power spectrum slopes at cluster scales. From the point of view of the FP, there is little difference between clusters that quietly accreted their mass and those that underwent massive mergers. The principal effect of strong mergers is to significantly change the ratio of the half-mass radius r(half) to the harmonic mean radius r(h).
An Integrated in Silico Analysis of Drug-Binding to Human Serum Albumin

Approaches such as quantitative structure-activity relationships (QSAR) and molecular modeling are integrated with the study of complex networks to understand drug binding to human serum albumin (HSA). A robust QSAR model using the topological substructural molecular descriptors/design (TOPS-MODE) approach has been derived and shows good predictability and interpretability in terms of structural contribution to drug binding to HSA. A perfect agreement exists between the group/fragment contributions found by TOPS-MODE and the specific interactions of drugs with HSA. These results indicate a preponderant contribution of hydrophobic regions of drugs to the specific binding to drug-binding sites 1 and 2 in HSA and specific roles of polar groups which anchor drugs to HSA binding sites. The occurrence of fragments contributing to drug binding to HSA can be represented by complex networks. The fragment-to-fragment complex network displays "small-world" and "scale-free" characteristics and in this way is similar to other complex networks including biological, social, and technological networks. A small number of fragments appear very frequently in most drugs. These molecular "empathic" fragments are good candidates for guiding future drug discovery research.
A Novel Colorectal Cancer Vaccine Consisting of Multiple Naturally Presented Peptides

Steffen Walter*, Sabrina Kuttruff*, Andrea Mayer*, Oliver Schoor*, Joerg Ludwig*, Frank Mayerw, Erika Hitrez, Bernhard Roessler*, Dominik Maurer*, Verona Vass*, Juha Lindner*, Nina Pawlowski*, Claudia Trautwein*, Joern Dengjel*, Norbert Hilf*, Toni Weinschenk*, Juergen Frisch*, Carsten Reinhardt*, Harpreet Singh-Jasuja*. *Immatics Biotechnologies, Tuebingen, Germany; wUniversity of Tuebingen, Tuebingen, Germany; zNational Institute of Oncology, Budapest, Hungary. To effectively treat cancer patients with T cell-based immunotherapy, T cells have to recognize peptides restricted by HLA molecules on tumors. For most of the published peptides it is unknown whether they are naturally presented or not. IMA910 is a novel peptide-based vaccine consisting of 10 HLA-A*02 binding and 3 HLA-DR binding tumor associated peptides (TUMAP), which were presented on colorectal tumors and were overexpressed in comparison to healthy tissues. 8 of the 10A*02-binding peptides had been confirmed to be naturally presented by peptide elution from surgically resected tumors and analysis by high-sensitivity mass spectrometry (XPRESIDENT approach). The two other A*02-binding peptides were chosen due to their characteristics described in literature. The multi-center clinical trial IMA910-101 enrolled 92 HLA-A*02+ advanced colorectal cancer (CRC) patients being at least clinically stable after 12 weeks of first-line oxaliplatin-based therapy. Patients were infused with a single low dose of cyclophosphamide (300mg/m) and repeatedly immunized intradermally (up to 16 vaccinations) with IMA910 in combination with GM-CSF (cohort 1; n=66) or IMA910 with GM-CSF plus topically applied imiquimod (cohort 2; n=26) as immunomodulators. Before and post vaccination patients were analyzed for T-cell responses to IMA910 HLA-A*02 and HLA-DR restricted peptides by HLA-multimer assay and intra-cellular cytokine (ICS) assay for CD8 T-cell responses and by ICS assay for CD4 T-cell responses. Tumor status of patients was monitored repeatedly by CT/MRI according to RECIST, corresponding tumor scans were reviewed centrally for assessment of disease control rate (DCR), progression-free survival (PFS) and overall survival (OS). IMA910 overall was immunogenic in 75/80 (94%) evaluable patients. A moderate but significant effect of imiquimod treatment on the number of immune responses to IMA910 peptides as detected by the ICS assay was observed. Finally, we demonstrate significantly increased PFS and a trend for increased OS in patients with class I immune responses to multiple TUMAPs. Most interestingly, only immune responses to peptides confirmed to be naturally presented were significantly associated with OS. Responses to the two immunogenic peptides included from literature with unclear status of natural presentation did not correlate and actually diluted the overall correlation of immune response with clinical benefit. This latter finding suggests that peptide antigens confirmed to be naturally presented may be preferable for vaccination and immunomonitoring.
Age of information: Design and analysis of optimal scheduling algorithms

Age of information is a newly proposed metric that captures delay from an application layer perspective. The age measures the amount of time that elapsed from the moment the mostly recently received update was generated until the present time. In this paper, we study an age minimization problem over a wireless broadcast network with many users, where only one user can be served at a time. We formulate a Markov decision process (MDP) to find dynamic transmission scheduling schemes, with the purpose of minimizing the long-run average age. While showing that an optimal scheduling algorithm for the MDP is a simple stationary switch-type, we propose a sequence of finite-state approximations for our infinite-state MDP and prove its convergence. We then propose both optimal off-line and online scheduling algorithms for the finite-approximate MDPs, depending on knowledge of time-varying arrivals.
Personalization revisited: a reflective approach helps people better personalize health services and motivates them to increase physical activity

Current approaches to personalization either presuppose people's needs and automatically tailor services or provide formulaic options for people to customize. We propose a complementary approach to personalization: a reflective strategy that helps people realize what matters to them and enables them to better personalize services themselves. To design this strategy, we first studied the practices of eight personal health service providers. We then tested the strategy's efficacy by building a Fitbit Plan website that encouraged Fitbit users to customize a plan or accept an automatically tailored plan. For one group of users, the website used the reflective strategy to assist in the plan setup process. A two-week between-subjects field experiment showed that the reflective strategy helped motivate users to carry out their plans, increasing their average daily steps by 2,425 steps. Without the reflective strategy, users either set easy goals or failed to carry out system-created plans, ultimately showing no change in their average daily steps. This work suggests that helping people reflect on and connect with their own goals in using a personalized service could advance the effectiveness of the service.
Real-time automatic emotion recognition from speech

In den vergangenen Jahren ist in der Mensch-Maschine-Kommunikation die Notwendigkeit, auf den emotionalen Zustand des Nutzers einzugehen, allgemein anerkannt worden. Um diesen automatisch zu erkennen, ist besonders Sprache in den Fokus geruckt. Bisher ging es dabei hauptsachlich um akademische und wenig anwendungsbezogene Untersuchungen, die auf im voraus aufgenommenen Datenbanken mit emotionaler Sprache beruhen. Die Anforderungen hierbei unterscheiden sich jedoch von denen der Online-Analyse, insbesondere sind im letzteren Fall die Bedingungen schwieriger und weniger vorhersagbar. Diese Dissertation beschaftigt sich mit der automatischen Erkennung von Emotionen aus Sprache in Echtzeit anhand akustischer Merkmale. Dazu wurden zunachst Experimente auf bestehenden Datenbanken mit emotionaler Sprache durchgefuhrt, um geeignete Methoden zur Segmentierung, Merkmalsextraktion und Klassifikation des Sprachsignals zu finden. Geeignet heist hierbei, dass die Methoden moglichst schnell und moglichst korrekt arbeiten. Um weitgehend allgemeingultige Ergebnisse zu erhalten, wurden die Experimente auf drei Datenbanken mit sehr unterschiedlichen Sprach- und Emotionstypen durchgefuhrt, namlich der Berlin Datenbank mit Emotionaler Sprache, dem FAU Aibo Emotionscorpus und dem SmartKom Mobile Corpus, die sowohl gelesene als auch spontane Sprache sowie gespielte und naturliche Emotionen enthalten. Die bei diesen Experimenten gewonnenen Erkenntnisse wurden dazu verwendet, eine umfassende Sammlung von Werkzeugen und Programmen zur Online- und Offline-Emotionserkennung, genannt EmoVoice, zu implementieren. Anhand von verschiedenen prototypischen Anwendungen und drei Benutzerstudien wurde die praktische Nutzbarkeit von EmoVoice, insbesondere auch durch externe Softwareentwickler, bewiesen. Weiterhin wurden vier Offline-Studien zur multimodalen Emotionserkennung durchgefuhrt, die akustische Merkmale mit Kontextinformation (Geschlecht), Biosignalen, Wortinformation und Mimik verbinden, da multimodale Erkennungsansatze eine hohere Erkennungsgenauigkeit versprechen.
Comparison of a highly automated 5-h susceptibility testing system, the Cobas-Bact, with two reference methods: Kirby-Bauer disk diffusion and broth microdilution

The results of susceptibility tests performed with the Cobas-Bact system were compared with those of the Kirby-Bauer disk diffusion and the broth microdilution methods. The evaluation included tests with 24 antibiotics against 250 isolates of the family Enterobacteriaceae and 13 antibiotics against 100 gram-positive cocci. Complete agreements between the Cobas-Bact and Kirby-Bauer methods were 82.8 and 84.5% for gram-positive cocci and gram-negative bacilli, respectively. Agreements between the Cobas-Bact and broth microdilution methods were 76.7% for gram-positive cocci and 84.8% for gram-negative bacilli. Complete agreements between the Kirby-Bauer and broth microdilution methods were 87.0% for gram-positive cocci and 92.2% for gram-negative bacilli. Despite generally satisfactory results with most organism-antibiotic combinations tested, additional modifications of the Cobas-Bact system are required to reduce the number of major and very major discrepancies, as well as to permit testing of Pseudomonas spp. and other gram-negative nonfermentative bacilli.
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM–HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley. edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley. edu/satchmo-js/supplementary/.
Phantom Acupuncture: Dissociating Somatosensory and Cognitive/Affective Components of Acupuncture Stimulation with a Novel Form of Placebo Acupuncture

In a clinical setting, acupuncture treatment consists of multiple components including somatosensory stimulation, treatment context, and attention to needle-based procedures. In order to dissociate somatosensory versus contextual and attentional aspects of acupuncture, we devised a novel form of placebo acupuncture, a visual manipulation dubbed phantom acupuncture, which reproduces the acupuncture needling ritual without somatosensory tactile stimulation. Subjects (N = 20) received both real (REAL) and phantom (PHNT) acupuncture. Subjects were retrospectively classified into two groups based on PHNT credibility (PHNTc, who found phantom acupuncture credible; and PHNTnc, who did not). Autonomic and psychophysical responses were monitored. We found that PHNT can be delivered in a credible manner. Acupuncture needling, a complex, ritualistic somatosensory intervention, induces sympathetic activation (phasic skin conductance [SC] response), which may be specific to the somatosensory component of acupuncture. In contrast, contextual effects, such as needling credibility, are instead associated with a shift toward relative cardiovagal activation (decreased heart rate) during needling and sympathetic inhibition (decreased SC) and parasympathetic activation (decreased pupil size) following acupuncture needling. Visual stimulation characterizing the needling ritual is an important factor for phasic autonomic responses to acupuncture and may undelie the needling orienting response. Our study suggests that phantom acupuncture can be a viable sham control for acupuncture as it completely excludes the somatosensory component of real needling while maintaining the credibility of the acupuncture treatment context in many subjects.
Political Ideology as a Predictor of Online Consumer Review Characteristics

As online consumer reviews have tremendously gained in importance for consumer decision-making and firm strategies, scholars have greatly advanced our understanding of the effect of various review characteristics on review helpfulness and product sales. However, the question of what actually causes variations in these review characteristics remains largely unexplored. This study addresses this gap and establishes a novel link between online reviews and reviewer personality by arguing that certain personality characteristics of reviewers play a crucial role in shaping the way reviews are composed. Specifically, we draw on an innovative and unobtrusive measure of personality in the context of online behavior by building on theory on political ideology. Numerous scholars have shown that individuals’ political ideologies are a result of stable, underlying personality characteristics. We hypothesize that, as a consequence, reviews by liberals exhibit more cognitively complex language, a greater diversity of arguments, more positively valenced language, a greater number of words, and a greater number of arguments compared to reviews by conservatives. By linking clickstream data to 245 online reviews, we provide support for our hypotheses. We discuss how the concept of political ideology can yield novel insights in online review research and how it allows website managers to provide more tailored incentives to potential reviewers.
Tumor-Infiltrating Immune Cells Promoting Tumor Invasion and Metastasis: Existing Theories

It is a commonly held belief that infiltration of immune cells into tumor tissues and direct physical contact between tumor cells and infiltrated immune cells is associated with physical destructions of the tumor cells, reduction of the tumor burden, and improved clinical prognosis. An increasing number of studies, however, have suggested that aberrant infiltration of immune cells into tumor or normal tissues may promote tumor progression, invasion, and metastasis. Neither the primary reason for these contradictory observations, nor the mechanism for the reported diverse impact of tumor-infiltrating immune cells has been elucidated, making it difficult to judge the clinical implications of infiltration of immune cells within tumor tissues. This mini-review presents several existing hypotheses and models that favor the promoting impact of tumor-infiltrating immune cells on tumor invasion and metastasis, and also analyzes their strength and weakness.
Variability in the CoRoT photometry of three hot O-type stars HD 46223, HD 46150, and HD 46966

Context. The detection of pulsational frequencies in stellar photometry is required as input for asteroseismological modelling. The second short run (SRa02) of the CoRoT mission has provided photometric data of unprecedented quality and time-coverage for a number of O-type stars. Aims. We analyse the CoRoT data corresponding to three hot O-type stars, describing the properties of their light curves and we search for pulsational frequencies, which we then compare to theoretical model predictions. Methods. We determine the amplitude spectrum of the data, using the Lomb-Scargle and a multifrequency HMM-like technique. Frequencies are extracted by prewhitening, and their significance is evaluated under the assumption that the light curve is dominated by red noise. We search for harmonics, linear combinations and regular spacings among these frequencies. We use simulations with the same time sampling as the data as a powerful tool to judge the significance of our results. From the theoretical point of view, we use the MAD non-adiabatic pulsation code to determine the expected frequencies of excited modes. Results. A substantial number of frequencies is listed, but none can be convincingly identified as being connected to pulsations. The amplitude spectrum is dominated by red noise. Theoretical modelling shows that all three O-type stars can have excited modes but the relation between the theoretical frequencies and the observed spectrum is not obvious. Conclusions. The dominant red noise component in the hot O-type stars studied here clearly points to a di erent origin than the pulsations seen in cooler O stars. The physical cause of this red noise is unclear, but we speculate on the possibility of sub-surface convection, granulation, or stellar wind inhomogeneities being responsible.