The passage indicates that science has proved that

Concept. A question of the form “the passage indicates / states that …” is a locating task, not a knowledge task. The answer is whatever the passage itself asserts, in the passage’s own terms — not what is generally true, not what sounds plausible, and not what the passage merely gestures at elsewhere. The governing rule is that the grammatical subject of the stem fixes which sentence must be read, and the predicate of that sentence is the answer.

Applying it here. The subject of the stem is what science has proved. The passage carries exactly one sentence that attributes a proof to science: “Science itself has proved that matter is energy, processes are as valid as facts, and affirmed the non-materiality of the universe.” The first predicate of that sentence is, word for word, matter is energy. That is therefore what the passage indicates science has proved.

Cross-checking the remaining claims against the passage:

• universe is material — the very same sentence asserts the reverse, that science “affirmed the non-materiality of the universe”, and the line immediately before it reads “The materialistic foundations of science have crumbled down.”

• nature has abundance — the passage’s only statement about the root of nature is that “quantity (measure) and quality (value) coexist at the root of nature”. Abundance is never claimed anywhere, and no such finding is attributed to science.

• humans are irresponsible — the closing line, “Human endeavours cannot afford to be humanistically irresponsible”, is a prescription about how human effort ought to be conducted, not a result science has proved.

Reading the stem’s subject straight onto the passage’s one sentence about scientific proof therefore gives: matter is energy.